Graphene FET devices, systems, and methods of using the same for sequencing nucleic acids

ABSTRACT

Provided herein are devices, systems, and methods of employing the same for the performance of bioinformatics analysis. The apparatuses and methods of the disclosure are directed in part to large scale graphene FET sensors, arrays, and integrated circuits employing the same for analyte measurements. The present GFET sensors, arrays, and integrated circuits may be fabricated using conventional CMOS processing techniques based on improved GFET pixel and array designs that increase measurement sensitivity and accuracy, and at the same time facilitate significantly small pixel sizes and dense GFET sensor based arrays. Improved fabrication techniques employing graphene as a reaction layer provide for rapid data acquisition from small sensors to large and dense arrays of sensors. Such arrays may be employed to detect a presence and/or concentration changes of various analyte types in a wide variety of chemical and/or biological processes, including DNA hybridization and/or sequencing reactions. Accordingly, GFET arrays facilitate DNA sequencing techniques based on monitoring changes in hydrogen ion concentration (pH), changes in other analyte concentration, and/or binding events associated with chemical processes relating to DNA synthesis within a gated reaction chamber of the GFET based sensor.

CROSS-REFERENCE TO RELATED APPLICATION

The present PCT application claims priority to U.S. Provisional PatentApplication No. 62/337,249, filed May 16, 2016, entitled “Graphene FETDevices, Systems, and Methods of Using the Same for Sequencing NucleicAcids,” the filing date and full disclosure of which is incorporatedherein by reference.

FIELD OF THE DISCLOSURE

The present disclosure relates, generally, to field effect transistors,such as integrated field-effect devices, systems including the devices,and methods of using the same for the analysis of biological and/orchemical materials, such as for molecular, e.g., nucleic acid, analysisand/or sequencing. More specifically, the present disclosure relates tofield effect transistors having a reaction layer that includes one ortwo-dimensional materials associated therewith.

BACKGROUND TO THE DISCLOSURE

The sequencing of Nucleic Acids, such as deoxyribonucleic acid (DNA) orRibonucleic acid (RNA), is a fundamental part of biological discovery.Such sequencing and/or the detection of the same is useful for a varietyof purposes and is often used in scientific research, as well as medicaladvancement. For instance, the genomics and bioinformatics fields areconcerned with the application of information technology and computerscience to the field of molecular biology. In particular, bioinformaticstechniques can be applied to process and analyze various genomic data,such as from an individual so as to determine quantitative andqualitative information about that data that can then be used by variouspractitioners in the development of diagnostic, prophylactic, and/ortherapeutic methods for detecting, preventing, or at least amelioratingdiseased states, and thus, improving the safety, quality, andeffectiveness of health care. The need for such diagnostic, therapeutic,and prophylactic advancements have led to a high demand for low-costsequencing, which in turn has driven the development of high-throughputsequencing, termed as Next generation sequencing (NGS).

Generally, the approach to DNA and/or RNA analysis, such as for geneticdiagnostics and/or sequencing, involves nucleic acid hybridization anddetection. For example, various typical hybridization and detectionapproaches include the following steps. Particularly, for geneticanalysis, a DNA or RNA sample of a subject to be analyzed may beisolated and immobilized on a substrate. In such instances, theimmobilized genetic material acts as a template for new nucleic acidsynthesis. A probe of a known sequence identity, e.g., a disease marker,may be labeled and washed across the substrate. If the disease marker ispresent, a binding event will occur, e.g., hybridization, and becausethe probe has been labeled the hybridization event may either be or notbe detected thereby indicating the presence or absence of the diseasemarker in the subject's sample.

For DNA sequencing, first, an unknown nucleic acid sequence to beidentified, e.g., a single-stranded sequence of DNA of a subject,composed of a combination of unknown nucleotides, e.g., a combination ofbase nucleotides of adenine, cytosine, guanine and thymine, or “As, Cs,Gs, and Ts,” is isolated, amplified, and immobilized on the substrate.Next, a known nucleotide labeled with an identifiable tag is contactedwith the unknown nucleic acid sequence in the presence of a polymerase.When hybridization occurs, the labeled nucleotide binds to itscomplementary base in the unknown sequence immobilized on the surface ofthe substrate. The binding event can then be detected, e.g., opticallyor electrically. These steps are then repeated until the entire DNAsample has been completely sequenced, e.g., sequencing by synthesis.Typically, these steps are performed by a next generation “Next Gen”sequencer wherein thousands to millions of sequences may concurrently beproduced in the next-generation sequencing process.

For example, a central challenge in DNA sequencing is assemblingfull-length genomic sequence data, e.g., of chromosomal sequences, froma sample of genetic material obtained from a subject. Particularly, suchassembling includes one or more genomic analysis protocols, such asemploying a mapping and/or an aligning algorithm, and involves mappingand aligning a fragment of identified sample sequence to a referencegenome, yielding sequence data in a format that can be compared to areference genomic sequence, such as to determine the variants in thesampled full-length genomic sequences. In particular, the methodsemployed in sequencing protocols do not produce full-length chromosomalsequences of the sample DNA.

Rather, in a typical sequencing protocol, sequence fragments, typicallyfrom 100-1,000 nucleotides in length, are produced without anyindication as to where in the genome they map and align. Therefore, inorder to generate full-length chromosomal genomic constructs, ordetermine their variance with respect to a reference genomic sequence,these fragments of DNA sequences need to be mapped, aligned, merged,and/or compared to the reference genomic sequence. Through suchprocesses the variants of the sample genomic sequences from thereference genomic sequences may be determined.

However, as the human genome is comprised of approximately 3.1 billionbase pairs, and as each sequence fragment is typically only from about100 to 500 to 1,000 nucleotides in length, the time and effort that goesinto building such full length genomic sequences and determining thevariants therein is quite extensive, often requiring the use of severaldifferent computer resources applying several different algorithms overprolonged periods of time. In a particular instance, thousands tomillions of fragments or even billions of DNA sequences are generated,mapped, aligned, and merged in order to construct a genomic sequencethat approximates a chromosome in length. A step in this process mayinclude comparing the sequenced DNA fragments to a reference sequence soas to determine where in the genome the fragments align.

In such instances, the raw genetic material must be processed so as toderive usable genetic sequence data therefrom. This processing may bedone manually or via an automated sequencer. Typically, such processinginvolves obtaining a biological sample from a subject, such as throughvenipuncture, hair, etc. and treating the sample to isolate the DNAtherefrom. Once isolated the DNA may be denatured, strand separated,and/or portions of the DNA may then be multiplied, e.g., via polymerasechain reaction (PCR), so as to build a library of replicated strandsthat are now ready to be sequenced, e.g., read, such as by an automatedsequencer, which sequencer is configured to “read” the replicatestrands, e.g., by synthesis, and thereby determine the nucleotidesequences that makes up the DNA. Further, in various instances, such asin building the library of replicated strands, it may be useful toprovide for over-coverage when preprocessing a given portion of the DNA.To perform this over-coverage, e.g., using PCR, may require increasedsample preparation resources and time, and therefore be more expensive,but it often gives an enhanced probability of the end result being moreaccurate.

More particularly, once the library of replicated strands has beengenerated they may be injected into an automated sequencer that may then“read” the strands, such as by synthesis, so as to determine thenucleotide sequences thereof. For instance, the replicated singlestranded DNA may be attached to a glass bead and inserted into a testvessel, e.g., an array. All the necessary components for replicating itscomplementary strand, including labeled nucleotides, are also added tothe vessel but in a sequential fashion. For example, all labeled “A”,“C”, “G”, and “T's” are added, either one at a time or all together tosee which of the nucleotides is going to bind at position one. Aftereach addition a light, e.g., a laser, is shone on the array. If thecomposition fluoresces then an image is produced indicating whichnucleotide bound to the subject location. More particularly, where thenucleotides are added one at a time, if a binding event occurs, then itsindicative fluorescence will be observed. If a binding event does notoccur, the test vessel may be washed and the procedure repeated untilthe appropriate one of the four nucleotides binds to its complement atthe subject location, and its indicative fluorescence is observed. Whereall four nucleotides are added at the same time, each may be labeledwith a different fluorescent indicator, and the nucleotide that binds toits complement at the subject position may be determined, such as by thecolor of its fluorescence. This greatly accelerates the synthesisprocess.

Once a binding event has occurred, the complex is then washed and thesynthesis steps are repeated for position two. For example, a markednucleotide “A” may be added to the mix to determine if the complement atthe position is a “T”, and if so, all the sequences having thatcomplement will bind to the labeled “T” and will therefore fluoresce,and the samples will all be washed. Where the binding happened the boundnucleotide is not washed away, and then this will be repeated for allpositions until all the over-sampled nucleic acid segments, e.g., reads,have been sequenced and the data collected. Alternatively, where allfour nucleotides are added at the same time, each labeled with adifferent fluorescent indicator, only one nucleotide will bind to itscomplement at the subject position, and the others will be washed away,such that after the vessel has been washed, a laser may be shone on thevessel and which nucleotide bound to its complement may be determined,such as by the color of its fluorescence. This continues until theentire strand has been replicated in the vessel.

A typical length of a sequence replicated in this manner is from about100 to about 500 base pairs, such as between 150 to about 400 basepairs, including from about 200 to about 350 base pairs, such as about250 base pairs to about 300 base pairs dependent on the sequencingprotocol being employed. Further, the length of these segments may bepredetermined, e.g., engineered, to accord with any particularsequencing machinery and/or protocol by which it is run. The end resultis a readout, or read, that is comprised of a replicated DNA segment,e.g., from about 100 to about 1,000 nucleotides in length, that has beenlabeled in such a manner that every nucleotide in the sequence, e.g.,read, is known because of its label. Hence, since the human genome iscomprised of about 3.1 billion base pairs, and various known sequencingprotocols usually result in labeled replicated sequences, e.g., reads,from about 100 or 101 bases to about 250 or about 300 or about 400bases, the total amount of segments that need to be sequenced, andconsequently the total number of reads generated, can be anywhere fromabout 10,000,000 to about 40,000,000, such as about 15,000,000 to about30,000,000, dependent on how long the label replicated sequences are.Therefore, the sequencer may typically generate about 30,000,000 reads,such as where the read length is 100 nucleotides in length, so as tocover the genome once.

However, in part, due to the need for the use of optically detectable,e.g., fluorescent, labels in the sequencing reactions being performed,the required instrumentation for performing such high throughputsequencing is bulky, costly, and not portable. For this reason, a numberof new approaches for direct, label-free detection of DNA hybridizationreactions have been proposed. For instance, among the new approaches aredetection methods that are based on the use of various electronicanalytic devices. Such direct electronic detection methods have severaladvantages over the typical NGS platform. For example, the detector maybe incorporated in the substrate itself, such as employing abiosystem-on-a-chip device, such as a complementary metal oxidesemiconductor device, “CMOS”. More particularly, in using a CMOS devicein genetic detection, the output signal representative of ahybridization event can be directly acquired and processed on amicrochip. In such an instance, automatic recognition is theoreticallyachievable in real time and at a lower cost than is currently achievableusing NGS processing. Moreover, standard CMOS devices may be employedfor such electronic detection making the process simple, inexpensive,and portable.

However, in order for next-generation sequencing to become widely usedas a diagnostic in the healthcare industry, sequencing instrumentationwill need to be mass produced with a high degree of quality and economy.One way to achieve this is to recast DNA sequencing in a format thatfully leverages the manufacturing base created for computer chips, suchas complementary metal oxide semiconductor (CMOS) chip fabrication,which is the current pinnacle of large scale, high quality, low-costmanufacturing of high technology. To achieve this, ideally the entiresensory apparatus of the sequencer could be embodied in a standardsemiconductor chip, manufactured in the same fab facilities used forlogic and memory chips. Recently, such a sequencing chip, and theassociated sequencing platform, has been developed and commercialized byIon Torrent, a division of Thermo-Fisher, Inc. The promise of this ideahas not been realized commercially due to the fundamental limits ofapplying a metal oxide semiconductor field effect transistor, or MOSFET,as a biosensor. When a MOSFET is used in solution as a biosensor, it isreferred to as an ISFET. A particular limitation, however, includes alack of sensor sensitivity and signal to noise characteristics as thesemiconductor node scales down to lower geometries of the transistor(gate length).

More particularly, a field effect transistor, FET, typically includes asource electrode and a drain electrode together forming a gate, andfurther including a channel region connecting the source and drainelectrodes. The FET may also include an insulating barrier separatingthe gate from the channel. The operation of a conventional FET relies onthe control of the channel conductivity, and thus the drain current, bya voltage, VGS, applied between the gate and source. For high-speedapplications, and for the purposes of increasing sensor sensitivity,FETs should respond quickly to variations in VGS. However, this requiresshort gates and fast carriers in the channel.

Unfortunately, FETs with short gates frequently suffer from degradedelectrostatics and other problems (collectively known as short channeleffects), such as threshold-voltage roll-off, drain-induced barrierlowering, and impaired drain-current saturation, results in a decreasein sensor sensitivity. However, scaling theory predicts that a FET witha thin barrier and a thin gate-controlled region (measured in thevertical direction) will be robust against short-channel effects down tovery short gate lengths (measured in the horizontal direction).Nevertheless, these effects make the use of such technologies difficultto employ in sequencing reactions.

Accordingly, the possibility of having channels that are very thin inthe vertical dimension would allow for high-speed transmission ofcarriers as well as for increased sensor sensitivity and accuracy. Whatis needed, therefore, is a FET device that is configured in such amanner as to include a shorter gate than is currently achievable inpresent FET applications, which will allow such technologies to be fullydeployed in sequencing reactions. Hence, a solution that includes such aFET device designed for use in biological applications, such as fornucleic acid sequencing and/or genetic diagnostics would especially bebeneficial.

SUMMARY OF THE DISCLOSURE

Provided herein are devices, systems, and methods of employing the samefor the performance of genomics and/or bioinformatics analysis. Thedevices, systems, and methods of the disclosure are directed in part tofield effect transistor (FET) sensors, integrated circuits, and arraysemploying the same for analyte measurements. The present FET sensors,arrays, and integrated circuits may be fabricated using conventionalCMOS processing techniques based on improved FET sensor and arraydesigns that increase measurement sensitivity and accuracy, and at thesame time facilitate significantly small sensor sizes and dense gFETsensor based arrays. Particularly, improved fabrication techniques, aswell as improved sensor devices, and their use, employing 1D or 2Dreaction layers, provide for rapid data acquisition from small sensorsto large, including dense arrays of sensors.

Such arrays may be employed to detect the presence of an analyte,changes in analyte concentration, and/or the identity of various analytetypes in a wide variety of chemical and/or biological processes,including DNA hybridization and/or sequencing reactions. Moreparticularly, presented herein are FET based sensor arrays that havebeen configured to facilitate DNA hybridization and sequencingtechniques, as well as the resultant detection of the same, which takeplace proximate a reaction zone that has been adapted to include a 1D or2D surface element. Specifically, in various embodiments, complementarymetal oxide semiconductor (CMOS) field effect transistor (FET) devicesare provided, where the devices include a plurality of reaction zonesthat have been adapted to have a 1D or 2D surface characteristicassociated therewith so as to decrease sensor length at the same time asincreasing sensor sensitivity. In such instances, the devices mayinclude a number of reaction zones that have been configured to receivea solution containing one or more reactants that when conditions aresuch to favor a reaction result in a detectable product.

Accordingly, presented herein are improved bio-chemical sensor devicesthat are configured for detecting changes in a solution that result fromthe occurrence of a binding event between two reactants proximate areaction zone of the device. In particular instances, the detectablechanges may be based on monitoring fluctuations in hydrogen ionconcentration (pH), variations in analyte concentration, and/or bindingevents associated with chemical processes relating to DNA synthesis,such as within a gated reaction chamber of a 1D or 2D based biosensorchip. More specifically, the present disclosure is at least in partdirected to a chemically-sensitive field-effect transistor for analysisof biological or chemical materials that solves many of the currentproblems associated with nucleic acid sequencing and geneticdiagnostics. Methods of fabricating such devices as well as their use inthe performance of biochemical reactions are also provided.

For instance, in one aspect of the present disclosure, achemically-sensitive transistor, such as a field effect transistor (FET)that is fabricated on a primary structure, such as a wafer, e.g., asilicon wafer, is provided. In various instances, the primary structuremay include one or more additional structures, for instance, in astacked configuration, such as including at least an insulator materiallayer. For example, the primary structure may include a secondarystructure, such as an insulator material, which may be included on topof, or otherwise be associated with, the primary structure, and may bean inorganic material, such as a silicon oxide, e.g., a silicon dioxide,or a silicon nitride, or an organic material, such as a polyimide, BCB,or other like material.

The secondary structure and/or insulator layer may include a furtherstructure containing one or more of a conductive source and/or aconductive drain, such as separated one from another by a space, andembedded in the primary and/or secondary structure materials and/or maybe planar with a top surface of the insulator. In various instances, thestructures may further include a processor, such as for processinggenerated data, such as sensor-derived data. Accordingly, the structuresmay be configured as, or otherwise include, an integrated circuit,and/or may be an ASIC, a structured ASIC, or an FPGA. In particularinstances, the structures may be configured as a complementarymetal-oxide semiconductor (CMOS), which in turn may be configured as achemically-sensitive FET containing one or more of a conductive source,a conductive drain, a gate, and/or a processor. For instance, the FETmay include a CMOS configuration having an integrated circuit that isfabricated on a silicon wafer, which may further be adapted to includean insulator layer. In such an instance, the insulator layer may includethe conductive source and drain such as where the source and drain arecomposed of metal, such as a damascene copper source and a damascenecopper drain.

In various instances, one or more of the structures may include asurface, e.g., a top surface, which surface may include a channel, suchas where the surface and/or channel may be configured to extend from theconductive source to the conductive drain. An exemplary length of thesurface and/or channel from the source to the drain may range from about0.001 microns to about 10 microns, such as from about 0.01 microns toabout 5 microns, for instance, from about 0.05 micron to 3 microns,including about 0.1 or about 0.5 microns to about 1 or about 1.5 orabout 2 microns in the horizontal and/or vertical directions. Anexemplary width of the surface and/or channel from side to side mayrange from about 0.001 microns to about 10 microns, such as from about0.01 microns to about 5 microns, for instance, from about 0.05 micronsto 3 microns, including about 0.1 or 0.5 microns to about 1 or about 1.5or about 2 microns.

Particularly, in particular instances, it may be useful to maximizeconductance, such as by decreasing the channel length, so as to increasethe sensitivity of the sensors, such as in a sensor array. For instance,to achieve enhanced transistor transconductance, the channel may beconfigured so as to include a short channel length, e.g., as short alength as possible, while at the same time including a larger channelwidth, e.g., as large as width as possible, within the sensor array, ina manner adapted for keeping the overall dimensions of the array ascompact as possible. For example, the equation for transconductance of afield effect transistor, such as for a transistor presented herein, is:g_(m)∝μC_(ov) W/L V_(sd); where g_(m) is the transconductance, μ is thecarrier mobility, C_(ov) is the overall capacitance of the oxide orother layers over the transistor, W is the channel width, L is thechannel length, and V_(sd) is the voltage from the source to the drain.Since g_(m) directly relates to the sensitivity of the sensor it may bedesirable to increase g_(m) through moderating the terms shown in theequation.

In particular increasing the W/L ratio (maximizing W and minimizing L)will increase g_(m). A preferred length of the channel from the sourceto the drain ranges is less than 1 micron, and more preferably is lessthan 500 nm, and more preferably is less than 50 nm, and more preferablystill is as short as the fabrication process will allow withoutgenerating defects or results that render the device unusable. The mostpreferable channel length will be 20 nm or less. Conversely, thepreferred width of the channel is as wide as possible. The width of thechannel in this case is not governed by the fabrication process as muchas by the design requirements of the overall sensor chip. It is likelythat many millions of sensors will be desired on the sensor chip. Withthis large number of sensors the individual sensor size and pitch (whichdirectly affects the channel width) must be kept reasonably smallotherwise the chip will so large as to be unable to be fabricated (e.g.,exceeds the photolithography reticle size) or too expensive (due to theeffect of defect density on a large chip size). A practical range ofchannel width is from 0.1 micron to 2 microns for a simple rectangularchannel design. In some cases it is desirable to increase the channellength to channel width ratio through the use of design techniques—forexample, an interdigitated tooth and comb design can provide for shortchannel lengths and large channel widths within a relatively compactarea.

In certain instances, the surface and/or channel may include aone-dimensional transistor material, a two-dimensional transistormaterial, a three-dimensional transistor material, and/or the like. Invarious instances, a one-dimensional (1D) transistor material may beincluded, which 1D material may be composed of a carbon nanotube or asemiconductor nanowire. In various instances, a two-dimensional (2D)transistor material may be included, which 2D material may be composedof a graphene layer, silicene, molybdenum disulfide, black phosphorous,and/or metal dichalcogenides. In various instances, the surface and/orchannel may further include a dielectric layer. In particular instances,the surface and/or channel may include a graphene layer.

Additionally, in various instances, a reaction layer, e.g., an oxidelayer, may be disposed on the surface and/or channel, such as layered orotherwise deposited on the 1D, 2D, e.g., graphene, or 3D layer, or thedielectric layer. Such an oxide layer may be an aluminum oxide or asilicon oxide, such as silicon dioxide. In some embodiments, the oxidelayer may have a thickness of about 20 nanometers, such as about 15nanometers, such as 10 or 9 or 7 or 5 nanometers or less. In variousinstances, a passivation layer may be disposed on the surface and/orchannel, such as layered or otherwise deposited on the 1D, 2D, or 3Dlayer and/or on an associated reaction layer on the surface and/orchannel. Such a passivation layer may have a thickness of about 0.5microns or less, such as about 0.1 microns or about 50 nanometers orabout 20 nanometers, such as about 15 nanometers, such as 10 or 9 or 7or 5 nanometers or less.

In particular instances, the primary and/or secondary structures may befabricated or otherwise configured so as to include a chamber or wellstructure in and/or on the surface. For instance, a well structure maybe positioned on a portion of a surface, e.g., an exterior surface, ofthe primary and/or secondary structures. In some instances, the wellstructure may be formed on top of, or may otherwise include, at least aportion of the 1D, 2D, and/or 3D material, and/or may additionallyinclude the reaction, e.g., oxide, and/or passivation layers. In variousinstances, the chamber and/or well structure may define an opening, suchas an opening that allows access to an interior of the chamber, such asallowing direct contact with the 1D, e.g., carbon nanotube or nanowire,2D, e.g., graphene, surface and/or channel. In such instances, the FETdevice may be configured as a solution gated sensor device.

Accordingly, a further aspect of the present disclosure is a bio-sensor.The bio-sensor includes a CMOS structure that may include a metalcontaining source, e.g., a damascene copper source, as well as a metalcontaining drain, e.g., a damascene copper drain, a 1D or 2D layered,e.g., a graphene layered, surface or channel extending from the sourceto the drain, and a well or chamber structure that may be positioned ona portion of an exterior surface of the 1D or 2D layered well. Inparticular instances, the well structure may be configured so as todefine an opening that allows for direct, fluidic contact with the 1D,e.g., nanotube, nanowire, and/or 2D, e.g., graphene, well or chambersurface. In various instances, an oxide and/or passivation layer may bedisposed in or on the chamber surfaces. Hence, in certain instances, achemically-sensitive transistor, such as a field effect transistor (FET)including one or more nano- or micro-wells may be provided.

In some embodiments, the chemically-sensitive field effect transistormay include a plurality of wells and may be configured as an array,e.g., a sensor array. Such an array or arrays may be employed such as todetect a presence and/or concentration change of various analyte typesin a wide variety of chemical and/or biological processes, including DNAhybridization and/or DNA or RNA sequencing reactions. For instance, thedevices herein described and/or systems including the same may beemployed in a method for the analysis of biological or chemicalmaterials, such as for whole genome analysis, genome typing analysis,micro-array analysis, panels analysis, exome analysis, micro-biomeanalysis, and/or clinical analysis, such as cancer analysis, NIPTanalysis, and/or UCS analysis. In a particular embodiment, one or moresurfaces within the wells of the field effect transistor may beconfigured as a reaction zone, which reaction zone may include anadditional structure, such as a graphene layer, and hence, the FET maybe a graphene FET (gFET) array.

Such FET sensors as herein described may be employed to facilitate DNAhybridization and/or sequencing techniques, such as based on monitoringchanges in hydrogen ion concentration (pH), changes in other analyteconcentrations, and/or binding events associated with chemical processes(e.g., relating to DNA synthesis), such as within a gated reactionchamber or well of the gFET based sensor, such as proximate the reactionzone(s). For example, the chemically-sensitive field effect transistormay be configured as a CMOS biosensor and/or may be adapted to increasethe measurement sensitivity and/or accuracy of the sensor and/orassociated array(s), such as by including one or more surfaces or wellshaving a surface layered with a 1D and/or 2D and/or 3D material, adielectric or reaction layer, a passivation layer, and the like. Inparticular instances, the increased sensitivity of the sensors may, inpart, be due to the presence of the presence of the 1D or 2D material,and/or further enhanced by its relationship to one or more of thereaction and/or passivation layers, which in turn allows for smallersensor configurations, therefore smaller channels and/or gates, and thusa greater density of sensors and/or arrays.

For instance, in a particular embodiment, a chemically-sensitivegraphene containing field effect transistor (gFET), such as a gFEThaving a CMOS structure is provided, where the gFET sensor, e.g.,biosensor, may include an oxide and/or passivation layer, such as alayer that is disposed on the surface of the well or chamber so as toincrease the measurement sensitivity and/or accuracy of the sensorand/or associated array(s). The oxide layer, when present, may becomposed of an aluminum oxide, a silicon oxide, a silicon dioxide, andthe like. More particularly, the oxide and/or passivation layers mayhave a suitable thickness such as from about 100 nm to about 75 nm, suchas from about 50 nm to about 30 nm, from about 40 nm to about 25 nm,such as from about 20 nm to about 10 nm or 9 nm or less, respectively.

In another aspect, the present FET integrated circuits, sensors, and/orarrays of the disclosure may be fabricated such as using any suitablecomplementary metal-oxide semiconductor (CMOS) processing techniquesknown in the art. In certain instances, such a CMOS processing techniquemay be configured to increase the measurement sensitivity and/oraccuracy of the sensor and/or array, and at the same time facilitatesignificantly small gates having relatively smaller sensor sizes andmore dense FET chamber sensor regions. Particularly, in variousembodiments, the improved fabrication techniques herein described resultin sensor devices containing reaction zones employing a 1D, 2D, 3Dlayers, and may further be manufactured and/or otherwise treated so asto contain one or more additional reaction layers, such as an oxideand/or passivation layers, which structures, along or in combinationprovide for rapid data acquisition, such as from small sensors to largeand dense arrays of sensors. In certain embodiments, one or more of suchlayers may be fabricated along with the manufacture of the array, suchas via one or more chemical vapor deposition techniques. Additionally,in particular embodiments, an ion-selective permeable membrane may beincluded, such as where the membrane layer may include a polymer, suchas a perfluorosulphonic material, a perfluorocarboxylic material, PEEK,PBI, Nafion, and/or PTFE. In some embodiments, the ion-selectivepermeable membrane may include an inorganic material, such as an oxideor a glass. In more particular embodiments, one or more of the variouslayers, e.g., the reaction, passivation, and/or permeable membranelayers may be fabricated or otherwise applied by a spin-coating,anodization, PVD, and/or sol gel method.

In a further aspect, a system is provided, such as a system configuredfor running one or more reactions so as to detect a presence and/orconcentration change of various analyte types in a wide variety ofchemical and/or biological processes, including DNA hybridization and/orsequencing reactions. As such, the system may include an array includingone or more, e.g., a plurality of sensors, such as where each of thesensors includes a chemically-sensitive field-effect transistor having aconductive source, a conductive drain, and a reaction surface or channelextending from the conductive source to the conductive drain. Inparticular instances, the array may include one or more wells configuredas one or more reaction chambers having the reaction surface or channelpositioned therein. In some instances, the surface and/or channel of thechamber may include a one-dimensional (1D) or two-dimensional (2D)transistor material, a dielectric or reaction layer, a passivationlayer, and/or the like.

The system may further include one or more of a fluidic component, suchas for performing the reaction, a circuitry component, such as forrunning the reaction processes, and/or a computing component, such asfor controlling and/or processing the same. For instance, a fluidicscomponent may be included where the fluidic component is configured tocontrol one or more flows of reagents over the array and/or one or morechambers thereof. Particularly, in various embodiments, the systemincludes a plurality of reaction locations, such as surfaces or wells,which in turn includes a plurality of sensors and/or a plurality ofchannels, and further includes one or more fluid sources containing afluid having a plurality of reagents and/or analytes for delivery to theone or more surfaces and/or wells for the performance of one or morereactions therein. In certain instances, a mechanism for generating oneor more electric and/or magnetic fields is also included.

The system may additionally include a circuitry component, such as wherethe circuitry component may include a sample and hold circuit, anaddress decoder, a bias circuitry, and/or at least one analog-to-digitalconverter. For instance, the sample and hold circuit may be configuredto hold an analog value of a voltage to be applied to or on a selectedcolumn and/or row line of an array of a device of the disclosure, suchas during a read interval. Additionally, the address decoder may beconfigured to create column and/or row select signals for a columnand/or row of the array, so as to access a sensor with a given addresswithin the array. The bias circuitry may be coupled to one or moresurfaces and/or chambers of the array and include a biasing componentsuch as may be adapted to apply a read and/or bias voltage to selectedchemically-sensitive field-effect transistors of the array, e.g., to agate terminal of the transistor. The analog to digital converter may beconfigured to convert an analog value to a digital value

A computing component may also be included, such as where the computingcomponent may include one or more processors, such as a signalprocessor; a base calling module, configured for determining one or morebases of one or more reads of a sequenced nucleic acid; a mappingmodule, configured for generating one or more seeds from the one or morereads of sequenced data and for performing a mapping function on the oneor more seeds and/or reads; an alignment module, configured forperforming an alignment function on the one or more mapped reads; asorting module, configured for performing a sorting function on the oneor more mapped and/or aligned reads; and/or a variant calling module,configured for performing a variant call function on the one or moremapped, aligned, and/or sorted reads. In particular instances, the basecaller of the base calling module may be configured to correct aplurality of signals, such as for phase and signal loss, to normalize toa key, and/or to a generate a plurality of corrected base calls for eachflow in each sensor to produce a plurality of sequencing reads. Invarious instances, the device and/or system may include at least onereference electrode.

Particularly, the system may be configured for performing a sequencingreaction. In such an instance, the FET sequencing device may include anarray of sensors having one or more chemically-sensitive field-effecttransistors associated therewith. Such transistors may include a cascodetransistor having one or more of a source terminal, a drain terminal,and or a gate terminal, such as composed of a damascene copper. In suchan instance, the source terminal of the transistor may be directly orindirectly connected to the drain terminal of the chemically-sensitivefield-effect transistor. In some instances, a one or two dimensionalchannel or other suitably configured surface element may be included andmay extend from the source terminal to the drain terminal, such as wherethe 1D channel material may be a carbon nanotube or nanowire, and thetwo-dimensional channel material may be composed of graphene, silicene,a phosphorene, a molybdenum disulfide, and a metal dichalcogenide. Thedevice may further be configured to include a plurality of column androw lines coupled to the sensors in the array of sensors. In such aninstance, each column line in the plurality of column lines may bedirectly or indirectly connected to or otherwise coupled to the drainterminals of the transistors, e.g., cascode transistors, of acorresponding plurality of sensors and/or pixels in the array, andlikewise each row line in the plurality of row lines may be directly orindirectly connected to or otherwise coupled with the source terminalsof the transistors, e.g., cascode transistors, of a correspondingplurality of sensors in the array.

In some instances, a plurality of source and drain terminals having aplurality of reaction surfaces, e.g., channel members, extended therebetween may be included, such as where each channel member includes aone or two or even three dimensional material. In such an instance, aplurality of first and/or second conductive lines, and so forth, may becoupled to the first and second source/drain terminals of thechemically-sensitive field-effect transistors in respective columns androws in the array, and so forth. Additionally, control circuitry may beprovided and coupled to the plurality of column and row lines such asfor reading a selected sensor connected to a selected column line and/ora selected row line. The circuitry may also include a biasing componenthaving a bias circuitry such as is configured to apply a read voltage,while the sample and hold circuit may be configured to hold an analogvalue of a voltage on a selected column line of the array during a readinterval. Particularly, the bias circuitry may be configured forapplying a read voltage to the selected row line, and/or to apply a biasvoltage such as to the gate terminal of a transistor, such as FET and/orcascode transistor of the selected sensor. In a particular embodiment,the bias circuitry may be coupled to one or more chambers of the arrayand be configured to apply a read bias to selected chemically-sensitivefield-effect transistors via the conductive column and/or row lines.Particularly, the bias circuitry may be configured to apply a readvoltage to the selected row line, and/or to apply a bias voltage to thegate terminal of the transistor, e.g., cascode transistor, such asduring a read interval.

A sense circuitry may also be included and coupled to the array so as tosense a charge coupled to one or more of the gate configurations of aselected chemically-sensitive field-effect transistor. The sensecircuitry may be configured to read the selected sensor based on asampled voltage level on the selected row and/or column line. In such aninstance, the sense circuitry may include one or more of a pre-chargecircuit, such as to pre-charge the selected column line to a pre-chargevoltage level prior to the read interval; and a sample circuit such asto sample a voltage level at the drain terminal of the selectedtransistor, such as during the read interval. A sample circuit mayfurther be included and contain a sample and hold circuit configured tohold an analog value of a voltage on the selected column line during theread interval, and may further include an analog to digital converter toconvert the analog value to a digital value.

In particular embodiments, the computer component of the FET, e.g.,CMOS, structure may include a processor configured for controlling theperformance of one or more reactions involving a biological or chemicalmaterial so as to obtain reaction results, and for analyzing thoseresults, for instance, based on detecting and/or measuring changes in avoltage (V) potential, current (I), or capacitance occurring on thechemically-sensitive field effect transistor. Particularly, theprocessor, such as a signal processor, may be configured so as togenerate one or more current (I) vs. voltage (V) curves, such as wherethe current I of the I-V curve is the current applied between the sourceand drain of the chemically sensitive field effect transistor and/orwhere the gate voltage (Vg) of the I-Vg curve is a gate or channelvoltage applied to the chemically-sensitive field effect transistor. Insuch an instance, the gate voltage Vg of the I-Vg curve is a top and/ora back gate voltage that may be applied to the chemically sensitivefield effect transistor through a top (or front) and/or back of thedevice, respectively. Hence, a suitably configured device of thedisclosure may be adapted as a front and/or back-gated device, which mayfurther be configured as a solution gate. Accordingly, in variousembodiments, a device of the disclosure may be a field-effect transistorthat includes a chamber adapted for measuring ion concentrations in asolution; such as where, when the ion concentration (such as H⁺ or OH⁻in a pH scale) within the chamber changes, the current through thetransistor, e.g., a gate region thereof, will change accordingly. Insuch an instance, the solution, when added to the chamber forms, orotherwise serves as, a gate electrode.

Hence, in specific embodiments, the gate voltage Vg of the I-Vg curvemay be a solution gate voltage such as applied to the chemicallysensitive field effect transistor through a solution flowed over aportion, e.g., a chamber, of the device. In some embodiments, thereference I-Vg curve and/or a chemical reaction I-Vg curve may begenerated in response to the biological material and/or chemicalreaction that is to be detected and/or occurs over or near thechemically-sensitive field effect transistor, such as within a chamberor well of the FET structure. In various embodiments, the processor maybe configured to determine differences in relationships between agenerated reference I-Vg curve and/or chemical reaction I-Vg curve. Incertain instances, the circuitry component may include at least oneanalog-to-digital converter that is configured for converting analogsignals, such as obtained as a result of the performance of thereaction(s) within the reaction well, or array of wells, into digitalsignals.

Accordingly, in another aspect, a chemically-sensitive field effecttransistor device may be provided, wherein the device may include astructure having a conductive source and drain as well as having asurface or channel or other functionally equivalent surface structureextending from the conductive source to the conductive drain, such aswhere the surface or channel may include a one-, two-, orthree-dimensional transistor material. The device may also include aprocessor such as where the processor is configured for generating areference I-Vg curve and/or generating a chemical reaction I-Vg curve,in response to the chemical reaction occurring within a chamber of thechemically-sensitive field effect transistor, and may be configured todetermine a difference between the reference I-Vg curve and the chemicalreaction I-Vg curve.

In some instances, the difference between the reference I-Vg curvemeasurement and the chemical reaction I-Vg curve measurement is a shiftin a minimum point of the Vg value of the chemical reaction I-Vg curverelative to a minimum point of the Vg value of the reference I-Vg curve.In other instances, the difference between the reference I-Vg curve andthe chemical reaction I-Vg curve is a shift in an ion value of thechemical reaction I-Vg curve relative to an ion value of the referenceI-Vg curve, for instance, where the ion values are taken from a p-typeor n-type section of the I-Vg curve. For example, the measurements ofthe slopes may be taken from the steepest and/or flattest sections onthe p-type and/or n-type portions of the I-Vg curves. In particularinstances, the difference between the reference I-Vg curve and thechemical reaction I-Vg curve is a shift in an Ioff value of the chemicalreaction I-Vg curve relative to an Ioff value of the reference I-Vgcurve. In one embodiment, the difference between the reference I-Vgcurve and the chemical reaction I-Vg curve is a change in the slope ofthe chemical reaction I-Vg curve relative to a change in the slope ofthe reference I-V g curve. In another embodiment, the difference betweenthe reference I-Vg curve and the chemical reaction I-Vg curve is anoverall change in shape of the chemical reaction I-Vg curve relative toan overall change in shape of the reference I-Vg curve. In otherembodiments, the difference in overall shape of the I-Vg curves isdetermined by first fitting a polynomial or other fitting line to eachof the I-Vg curves and then comparing the coefficients of those fittinglines. In other embodiments, the difference between a reference I-Vgcurve and the chemical reaction I-Vg curve is based on more than onechemical reaction I-V g curve.

Accordingly, in particular embodiments, the FET and/or processor may beconfigured to respond to a shift in the I-V or I-Vg curve, such as wherethe curve is shifted in response to the detection of a biologicalcompound and/or the result of a reaction taking place in or on a surfaceof the FET device. In some instances, the I-V/I-Vg curve may be producedand/or shifted in response to a chemical reaction occurring on areaction layer and/or the surface of a 1D or 2D, e.g., graphene, surfaceof the field effect transistor, such as resulting from the detection ofa biological compound or reaction occurring within the well structure ofthe device. Hence, the FET and/or processor may be configured so as toshift the I-V curve or I-Vg curve such as in response to the chemicalreaction. In various embodiments, one or more elements and/or methods,as herein described, may be used to shift a reference I-V or I-Vg curveand/or a chemical reaction I-Vg curve so that the difference between thereference I-Vg curve and a chemical reaction I-Vg is more pronounced.For instance, the device may include a structure, such as a membrane,other surface layer, and/or other element configured for enhancing theability of the processor to determine the difference between various I-Vand/or I-Vg curves.

Hence, in a further aspect, a chemically-sensitive FET transistor thatis fabricated on a primary structure having a stacked configurationincluding an inorganic base layer, e.g., a silicon layer; a dielectricand/or an organic or inorganic insulator layer, such as a silicondioxide layer; a 1D, 2D, or 3D material layer, such as a carbonnanotube, nanowire, or graphene layer; a reaction, e.g., oxidation,and/or passivation layer; and further having a conductive source anddrain embedded in one or more of the layers, such as between and/orforming a gate structure, e.g., a solution gate region, may be provided.In various embodiments, the gate region may be configured so as to forma chamber or well and the 1D or 2D material and/or oxidation layers maybe positioned between the conductive source and drain in such a manneras to form a bottom surface of the chamber. The structures may furtherinclude or otherwise be associated with an integrated circuit and/or aprocessor, such as for generating and/or processing generated data, suchas sensor derived data.

Accordingly, in particular embodiments, a further structured layer,e.g., a secondary or tertiary structure, may also be provided, such aswhere the further structured layer may be included and/or present withinthe well or chamber, such as to enhance the ability of the processor todetermine the difference between the current and/or voltages as well astheir respective associated curves. More particularly, the additionalstructure may include an ion-selective permeable membrane, such as anion-selective permeable membrane that allows ions of interest to passthrough the membrane while blocking other ions, such as to enhance theability of the processor to determine the difference between thereference I-V or I-Vg curve and the chemical reaction I-V or I-Vg curve,and thus enhance the ability of the processor to detect a desiredchemical reaction. In various instances, the FET may be configured suchthat the I-V or I-Vg curve(s) may be shifted so as to better respond to,detect, and/or otherwise determine a biological compound and/or achemical reaction, such as a biological compound and/or a chemicalreaction occurring on the 1D or 2D, e.g., graphene, surface of thechemically-sensitive field effect transistor. In particular instances,the ion-selective permeable membrane may include a 2D transistormaterial, e.g., graphene, which may or may not be electrically connectedto the source and/or drain layer and/or channel.

Accordingly, in various instances, the ion-selective permeable membranemay be positioned within the well and/or over a passivation layer, anion sensitive or reaction layer, a 1D and/or a 2D transistor materiallayer, and/or a dielectric layer that itself may be positioned overand/or otherwise form a part of the chamber or channel. In certainembodiments, the membrane layer may be or otherwise be associated withan ion getter material, such as an ion getter material that traps ionsthat may or may not be relevant to the biological species and/orchemical reaction to be sensed and/or determined, such as to enhance theability of the processor to determine the difference between thereference I-V or I-Vg curve and/or the chemical reaction I-V or I-Vgcurve, e.g., because there are fewer interfering ions, thus enhancingthe ability of the processor to detect the desired biological speciesand/or results of the chemical reactions. Particularly, the ion gettermaterial may be arranged within proximity to the chamber and/or surfacethereof so that the action of gettering the unwanted ions improves thedetection capability of the chemically-sensitive field effecttransistor. In some instances, one or more of the various layers herein,such as the ion getter material may be placed over one or more of theother layers, such as the dielectric layer, oxide layer, or 1D or 2D or3D layers, positioned in proximity to one or more of the chambers,channels, or surfaces of the FET device.

In particular instances, an additional material, e.g., HMDS, may beincluded so as to manage the interaction of the chamber and/or channeland/or associated oxide layer and/or underlying 1D or 2D or 3Dtransistor layer. For instance, a chemically-sensitive field effecttransistor of the disclosure may include a secondary or tertiarystructure that includes a 2D transistor channel or surface which mayinclude an ion-sensitive material over the channel or surface. In suchan instance, the material may be sensitive to ions that are differentfrom the ions associated with the biological molecule or chemicalreaction that is to be detected. Particularly, in some instances, theaction of sensing ions that are different from the ions associated withthe biologics and/or chemical reactions that are to be detected allowsthe processor to filter out the signal from the unwanted ions from thesignal of the ions of interest.

In a further aspect of the present disclosure, a system having achemically-sensitive transistor, such as a field effect transistor (FET)including one or more chambers, e.g., a plurality of chambers having awell structure(s) formed therein is provided. In such an instance, thewell(s) may be structured as a reaction location, wherein one or morechemical reactions may take place. In such an embodiment, the system mayinclude a fluidics component having a fluid source, e.g., a reservoir,containing one or more fluids therein and configured for delivering thefluid from the reservoir to the reaction chamber, such as for thedetection of a biologic and/or the performance of one or more chemicaland/or biological reactions, such as a nucleic acid sequencing reaction.Hence, the fluidics component, e.g., the fluid source, may be in fluidiccommunication with the FET device configured for biological and/orchemical analysis.

Accordingly, in certain instances, the fluid may include one or morereactants, such as one or more analytes necessary for performing asequencing reaction, as herein described. In a particular embodiment,the fluid may include one or more, e.g., a plurality of microbeads,having a nucleic acid template attached thereto, for instance, where thetemplate is a DNA or RNA molecule to be sequenced, and the fluidcontaining the microbead is to be delivered to the well such as forcarrying out the sequencing reaction. In such an embodiment, one or moreof, e.g., each, of the plurality of microbeads may be configured so asto have electric charge and/or paramagnetic properties. The device mayadditionally include an electric and/or magnetic field component, e.g.,having an electric and/or magnetic field generator, such as where theelectric and/or magnetic field component is configured to generate anelectric and/or magnetic field so as to interact with the electricand/or magnetic charge properties of each of the plurality of microbeadsto attract the microbeads into a reaction location, such as a reactionsurface, a channel, a well, a chamber, and/or a sensor of the FETdevice, such as by using electrophoresis and/or magnetism.

Hence, one or more, e.g., a plurality of microbeads, may be drawn ontoor into a reaction location of the plurality of reaction locations,which locations may be formed as wells, e.g., one or more thin wells.The microbeads may include an analyte such as a biological material or achemical material, e.g., one or more nucleotide sequences. Particularly,a fluid containing the analyte containing microbeads may be introducedinto the wells, such as by a fluidics component of the disclosure. Asthe analyte may be a nucleic acid sequence having negative chargeproperties, an electric and/or magnetic field may be appliedindividually or collectively to the wells, so as to draw an analytecontaining microbead onto each reaction location, e.g., into each wellor sensor containing channel. In various instances, the electric and/ormagnetic field component generates an electric and/or magnetic field soas to interact with the electric charge properties of the microbeadthereby drawing it to the reaction location. In certain instances, themicrobead itself may be charged and/or may have electric and/or magneticproperties, and thereby may be drawn to the reaction location usingelectrophoresis and/or magnetism.

The use of electrophoresis and/or magnetism allows for thinner reactionlocation structures. In particular instances, therefore, an electricand/or magnetic field generator may be configured for drawing and/orpositioning a microbead within the well structure, such as in proximityto a channel or chamber of the device, and in other instances, theelectric and/or magnetic field generator may be configured for reversingthe electrical and/or magnetic field so as to repulse the microbead fromthe reaction location, channel, and/or chamber. In various instances, anarray of reaction locations may be provided each having a magnet thatallows for selective filling of the reaction locations with differentnumbers and/or types of microbeads, such as at select reactionlocations. In such an instance, multiple electric and/or magnetic fieldgenerators for selective filling of reaction locations, e.g., wells.

Accordingly, one aspect of the present disclosure is a system and/or amethod for positioning one or more, e.g., a plurality, of microbeads,e.g., containing one or more DNA and/or RNA templates attached thereto,within a reaction or plurality of reaction locations for biological orchemical analysis, such as for nucleic acid sequencing. The system mayinclude a CMOS FET device having an integrated circuit structureconfigured for performing a biological or chemical analysis, such aswithin a plurality of nano- or micro-reaction wells, as described above,having a fluidic component, a circuitry component, and/or a computingcomponent, and the method may include one or more of the followingsteps.

For instance, the method may include the fluidic component introducing afluid to be in contact with the device, such as where the fluidicscomponent is configured to control a flow a fluid of reagents over thearray, and the fluid may include one or more microbeads that may haveelectric charge and/or paramagnetic properties. In such an instance, thedevice may include an integrated circuit structure, a plurality ofreaction locations having one or more wells, a plurality of sensorsand/or a plurality of channels, and/or an electric and/or magnetic fieldcomponent. The electric field and/or magnetic field component may beconfigured to activate the electronic and/or magnetic field, and themethod may also include activating an electric and/or magnetic field soas to interact with the electric and/or paramagnetic properties of eachof the microbeads. The method may additionally include drawing the oneor more microbeads into a reaction location of the plurality of reactionlocations using electrophoresis and/or magnetism. In certain instances,the method may include positioning the one or more microbeads within theone or more reaction locations for biological or chemical analysis.

In particular instances, the electric and/or magnetic fields may begenerated by the plurality of electric and/or magnetic field generators,e.g., included in the integrated circuit structure, in all or only asubset of the plurality of reaction locations so as to only attract aplurality of microbeads to the subset of reaction locations, such as forselectively filling the plurality of reaction locations with theplurality of microbeads. In such an instance, different types ofmicrobeads may be attracted to different reaction locations, such as bypulsing the voltage and/or magnetic generators and/or keeping the sameconstant. Particularly, where an electric field generator is providedthe voltage applied to the device may be variable or constant and may beless than about 10V, such as about less than 8V, or less than about 6V,including less than about 4V or about 2V or 1V. The voltage may beapplied between a location above the fluid and a location on or belowthe reaction location, such as above the package lid and/or below themetal plate below the package. In certain instances, the location belowthe reaction location may be a metal or conductive layer such as withinthe package or package substrate. The method may also include the stepof reversing the electric or magnetic field so as to eject the pluralityof beads from the plurality of wells, sensors, and/or channels, eitherentirely or selectively.

Further, as indicated, each or a subset of the plurality of reactionlocations may be utilized to generate electric fields to attract amicrobead thereby allowing for programmability to each or a subset ofreaction locations, for instance, 99% or 95% or 90% or 85%, or 80% orless of the plurality of wells are occupied with a microbead. Hence, theelectric and/or magnetic field may be generated in only a subset of theplurality of wells, sensors or channels to only attract a plurality ofmicrobeads to the subset. Likewise, a plurality of electric and/ormagnetic field generators for selective filling the plurality of wells,sensors or channels with the plurality of microbeads, and/or ejectingthe plurality of beads from the plurality of wells, sensors or channels.In such an instance, the electric and/or magnetic field generator may bean electric source, a permanent magnet and/or an electromagnet. Asindicated, the plurality of magnetic field generators is configured toreverse the magnetic field to eject the plurality of microbeads from theplurality of reaction locations or a subset thereof.

Additionally, in one aspect of the present disclosure, a device, system,and/or method for verifying well occupancy for a plurality of wells foranalysis of biological or chemical materials may be provided. Forinstance, a device of the system may include a plurality of wells havinga plurality of sensors, such as where each well includes a graphenelayer, and each sensor is configured as a field effect transistor. Insuch instances, the system may include a device for receiving a fluidcontaining the plurality of microbeads. Particularly, the device mayinclude a processor, a CMOS structure having an integrated circuit, aplurality of wells, and a plurality of sensors within the CMOSstructure. Each of plurality of wells may be configured to receive amicrobead of the plurality of microbeads, and the CMOS structure mayinclude a mechanism for drawing and/or ejecting the beads into or out ofthe wells. Hence, the method may include the step of flowing theplurality of microbeads over and/or into the plurality of reactionlocations and/or wells and/or may include determining, e.g., throughelectrical and/or magnetic sensing if a reaction location and/or well isoccupied or unoccupied and/or if a well contains one or multiplemicrobeads.

Consequently, the processor may be configured to determine if a well isunoccupied and/or if the well contains one or more, e.g., multiplemicrobeads. In certain instances, the processor may also be configuredto eliminate or modify one or more of the measurements, such as based onthe number of wells occupied or unoccupied, e.g., the number of wellscontaining none, one or multiple microbeads. For instance, the processormay be configured to eliminate from the measurement the number of wellsunoccupied and the number of wells containing multiple microbeads, orcompensate in the measurement for the number of wells unoccupied and thenumber of wells containing multiple microbeads, and the like.

In such instances, the measurement may be a shift in an I-V or I-Vgcurve. In particular instances, the processor may be configured toeliminate from the measurement the number of wells unoccupied and thenumber of wells containing one or multiple microbeads and/or tocompensate in the measurement for the number of wells unoccupied and thenumber of wells containing one or multiple microbeads. Accordingly, insome embodiments, the measurement may be a shift in an I-V or I-Vgcurve, such as one or more of: generating a plurality of I-V or I-Vgcurves so as to determine a shift in response to a chemical reactionoccurring on or near the chemically-sensitive field effect transistor;generating a chemically-sensitive field-effect transistor I-V or I-Vgcurve in response to a chemical reaction occurring on or near thechemically-sensitive field-effect transistor so as to detect a change inthe slope of the I-V curve; and/or to sense shifts in a capacitance as afunction of a gate voltage.

Having briefly described the present technology, the above and furtherobjects, features and advantages thereof will be recognized by thoseskilled in the pertinent art from the following detailed description ofthe invention when taken in conjunction with the accompanying drawings.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1A is an illustration of a substrate for use in achemically-sensitive field-effect transistor, such as for a system foranalysis of biological and/or chemical materials. In this instance, thesubstrate includes an insulating layer having a source and a drain, andfurther includes a reaction zone having a graphene layer associatedtherewith.

FIG. 1B is an illustration of a graphene layer, such as for use in thesubstrate of FIG. 1A.

FIG. 1C is an illustration of molybdenum disulfide.

FIG. 1D is an illustration of black phosphorous.

FIG. 1E is an illustration of silicone.

FIG. 1F is an illustration of a nanotube.

FIG. 1G is an illustration of a semiconductor nanowire structure.

FIG. 1H is an illustration of a graphene layered substrate of FIG. 1Aconfigured as a chemically-sensitive field-effect transistor having areaction layer associated with the graphene layer, such as for use in asystem for analysis of biological and/or chemical materials.

FIG. 1I is an illustration of a chemically-sensitive field-effecttransistor of FIG. 1A having a silicon dioxide layer positioned over thesubstrate and insulating layers, and further having a well structureetched into the silicon dioxide layer so as to form a chamber proximatethe graphene layered reaction zone. In this instance, the chamberincludes a passivation layer or etch stop layer placed over the reactionlayer.

FIG. 2A is an illustration of a chemically-sensitive field-effecttransistor having a graphene layered well structure, such as for asystem for analysis of biological and/or chemical materials.

FIG. 2B is an illustration of a chemically-sensitive field-effecttransistor of FIG. 2A, having a graphene layered well structure thatfurther includes a reaction layer associated with the graphene layer,such as for a system for analysis of biological and/or chemicalmaterials.

FIG. 2C is a top plan view of a chemically-sensitive field-effecttransistor with a well structure.

FIG. 2D is a top plan view of a chemically-sensitive field-effecttransistor with another configuration of a well structure.

FIG. 2E is a top plan view of an array for a system for analysis ofbiological or chemical materials, where the array includes multiplechemically-sensitive field-effect transistors.

FIG. 3A is a block diagram of a system for analysis of biological orchemical materials.

FIG. 3B is a block diagram of a circuitry component for a system foranalysis of biological or chemical materials.

FIG. 3C is a block diagram of a computing component for a system foranalysis of biological or chemical materials.

FIG. 4A is an illustration of a chemically-sensitive field-effecttransistor of FIG. 2A, having a graphene layered well structure thatincludes a nano- or micro-bead therein.

FIG. 4B is an illustration of a chemically-sensitive field-effecttransistor of FIG. 4A, having a graphene layered well structure thatincludes a reaction layer associated with the graphene layer, whichfurther includes a nano- or micro-bead therein.

FIG. 4C is an illustration of a chemically-sensitive field-effecttransistor of FIG. 4A, having a graphene layered well structure thatincludes a plurality of nano- or micro-beads therein.

FIG. 5A is an illustration of the substrate of FIG. 1A, having a silicondioxide layer positioned above a graphene layered reaction zone, andutilizing a magnetic field for the positioning of a nano- or micro-beadto be associated therewith.

FIG. 5B is an illustration of the substrate of FIG. 1D, having a silicondioxide layer positioned above a graphene layered reaction zone, andutilizing a magnetic field for the positioning of a nano- or micro-beadto be associated therewith.

FIG. 5C is an illustration of the substrate of FIG. 5B, in an alternateconfiguration, such as utilizing a magnetic field reversal of a magnetto release a nano- or micro-bead.

FIG. 5D is an illustration of the chemically-sensitive field-effecttransistor of FIG. 4A, such as for a system for analysis of biologicalor chemical materials, utilizing an electric field for positioning of anano- or micro-bead.

FIG. 5E is an illustration of an array of chemically-sensitivefield-effect transistors for a system for analysis of biological orchemical materials utilizing multiple magnets for generating a pluralityof magnetic fields for positioning of nano- or micro-beads within thewells.

FIG. 6A is a graph of an I-Vg curve with characteristics that are usedto categorize I-V g curves.

FIG. 6B is a graph of an I-Vg curve illustrating a single difference ormultiple differences.

FIG. 6C is a graph of an I-Vg curve illustrating a shift in the I-Vgcurve.

FIG. 6D is a graph of an I-Vg curve illustrating a change in the shapeof the I-Vg curve.

FIG. 6E is a graph of an I-Vg curve illustrating a change in the levelof the I-Vg curve (Ion in p-type region).

FIG. 6F is a graph of an I-Vg curve illustrating a change in the levelof the I-Vg curve (Ion in n-type region).

FIG. 6G is a graph of an I-Vg curve illustrating a change in the levelof the I-Vg curve (Ioff).

FIG. 6H is a graph of an I-Vg curve illustrating a fit polynomial orother fitting line to curve and use coefficients as read criterion.

FIG. 6I is a graph of an I-Vg curve illustrating a check-slope of theI-Vg curve on one or both sides (Gm & proportional to mobility), and useof a solution gate and backgate in combination to improve a signal andmove the curve where desired.

FIG. 7A is a graph of an I-Vg curve for various pH values.

FIG. 7B is a graph of current increase vs. pH increase.

FIG. 7C is a graph of frequency vs. normalized power spectral densityfor silicon ISFET.

FIG. 7D is a graph of frequency vs. normalized power spectral densityfor a typical graphene FET.

FIG. 7E is a graph of frequency vs. normalized power spectral densityfor a graphene FET of the present invention.

FIG. 7F is a graph of noise vs. bias voltage.

FIG. 7G is a graph of Dirac voltage vs. current increase.

FIG. 8A is an illustration of a chemically-sensitive field-effecttransistor with a graphene layered well structure and having a permeablemembrane associated with the graphene layer.

FIG. 8B is a graph of an average sensitivity of a graphene FET (“GFET”)calculated as a function of liquid gate potential.

FIG. 9A is an illustration of electrowetting for biomolecule attachment.

FIG. 9B is an illustration of electrophoresis for biomoleculeattachment.

FIG. 9C is an illustration of microfluidics for biomolecule attachment.

FIG. 9D is an illustration of an optical readout of DNA sequencing usingnanomaterials.

FIG. 10A is a block diagram of components for a system for analysis ofbiological or chemical materials.

FIG. 10B is an illustration of an exemplary graphene field-effecttransistor and chip.

FIG. 11 is an illustration of various planar source and drain electrodedesigns, including interdigitated designs.

FIG. 12 is a cross-section of a well opening stopping on ananalyte-sensitive layer.

FIG. 13 is an illustration highlighting a second analyte-sensitive layercoating the walls of a well.

FIG. 14 is an illustration of using the well walls to create 3Dinterdigitated electrodes.

FIG. 15 is an illustration of the well structure of FIG. 14 with atransistor material or an analyte-sensitive layer.

FIG. 16 is a picture showing a metal pattern in a deep trench created byphotolithography.

FIG. 17 is an illustration of a top plane view of a source and drainelectrodes at the bottom of a well.

FIG. 18 is an illustration of using alternating vertical metal layers tocreate an interdigitated type of effect to maximize the of ratio channelwidth to channel length.

FIG. 19 is an illustration of the structure of FIG. 18 with a transistormaterial or an analyte-sensitive layer.

FIG. 20 is an illustration of using alternating vertical layers of metaland transistor material to create an interdigitated type of effect tomaximize the ratio of channel width to channel length.

FIG. 21 is an illustration of process steps that may be used to createthe structure shown in FIG. 20.

FIG. 22 is an illustration of how vias or chambers in the transistorchannel material may be formed thus allowing for edge contact to thechannel material.

FIG. 23 is an illustration of a well that uses carbon nanotubes tocreate interdigitated transistors in a vertical direction.

Having briefly described the present technology, the above and furtherobjects, features and advantages thereof will be recognized by thoseskilled in the pertinent art from the following detailed description ofthe invention when taken in conjunction with the accompanying drawings.

DETAILED DESCRIPTION OF THE DISCLOSURE

Accordingly, provided herein are devices, systems, and methods ofemploying the same for the performance of one or more chemical and/orbioinformatics analysis operations. Particularly, the devices, systems,and methods of the disclosure are directed in part to 1D, 2D, or 3Dfield effect transistor (FET) sensors, integrated circuits, and arraysemploying the same for analyte measurements. The present FET sensors,arrays, and integrated circuits may be fabricated using conventionalCMOS processing techniques based on improved 1D, 2D, or 3D FET sensorand array designs that increase measurement sensitivity and accuracy,and at the same time facilitate significantly small sensor sizes anddense sensor array designs.

More particularly, such improved fabrication techniques employing 1D,2D, e.g., graphene, or 3D materials as a reaction layer provide forrapid data acquisition from small sensors to large and dense arrays ofsensors. Such arrays may be employed to detect the presence and/orconcentration changes of various analyte types in a wide variety ofchemical and/or biological processes, including DNA hybridization,and/or nucleotide and/or protein sequencing reactions. Accordingly, inparticular examples, graphene Field Effect Transistor (gFET) arraysfacilitate genetic and/or protein sequencing techniques based onmonitoring changes in various reactants within a zone associated withthe array, such as changes in ion concentration, e.g., changes inhydrogen ion concentration (pH), or changes in other analyteconcentrations, and/or binding events associated with chemical processesrelating to sequencing synthesis, such as within a gated reactionchamber of the gFET based sensor. Particularly, the present disclosureis a chemically-sensitive graphene layered field-effect transistor foranalysis of biological and/or chemical materials that solves many of thecurrent problems associated with nucleic acid sequencing, genetic,and/or bioinformatics diagnostics.

Accordingly, provided herein is a system for analysis of biologicaland/or chemical materials. In various embodiments, the system includes asubstrate, where the substrate includes one or more chamber and/orchannel arrangements therein, such as where the chamber and/or a channelthereof may be associated with one or more sensors. In particularinstances, a solution gated well structure is provided, such as wherethe well structure may be configured such that a biological and/orchemical reaction may take place within the well, such as proximate achannel structure therein. In various instances, the well is positionedon a portion of the substrate so as to align with an exterior surface ofthe channel of each sensor, such as where the well structure defines anopening allowing for direct fluid contact with the channel.

In various instances, the length of the interior surface, e.g., thechannel, of the well, such as from the source to the drain may rangefrom 0.05 micron to 3 microns, and a width of the surface and/or channelmay range from 0.5 micron to 2 microns. In particular instances, thewell structure may be configured to include or otherwise be associatedwith a nucleic acid template, such as a nucleic acid that may bedirectly or indirectly immobilized on a surface of the well. Forinstance, in certain instances, the nucleic acid template may be boundto an interior surface of the well chamber, such as on the substrateitself, or a layer associated therewith, e.g., a layer composed of aone- or two-dimensional transistor material. In various embodiments, thenucleic acid template may be bound to a secondary substrate, such as abead positioned within the well, such as proximate the graphene layer.

Accordingly, in one aspect of the present disclosure, the sensorsubstrate may be configured as a chemically-sensitive field-effecttransistor (FET). Particularly, in certain implementations, a fieldeffect transistor may be provided, such as where the FET includes achamber having a channel structure incorporated therein. In particularembodiments, the chamber and/or the channel and/or a structure thereofmay be optimized in such a manner so as to maximize the ratio of channelwidth (W) to channel length (L). For instance, the channel may include a1D or 2D or 3D structure, such as where the channel and/or the channelstructure includes a geometry that has been optimized to maximize theratio of channel width (W) to channel length (L). This can be donethrough the use of interdigitated source and drain electrode geometriesin a single plane or through the use of 2D and/or 3D electrodestructures.

In such an instance, the transistor may include a conductive source anda conductive drain forming the channel structure, which channelstructure extends from the conductive source to the conductive drain. Insuch an instance, the opening of the well is positioned in relation tothe channel so that the opening aligns with the positioning of thesource and drain, and more particularly with the associated sensor. Asindicated, in various embodiments, a bounding surface of the wellincludes a one-dimensional (1D) transistor material, such as a carbonnanotube (CNT) or a semiconductor nanowire, or a two-dimensional (2D)transistor material, such as composed of graphene, molybdenum disulfide,other metal dichalcogenides, and black phosphorous. In variousinstances, a three-dimensional (3D) structure may be included such asset forth in FIG. 11.

For example, the transconductance through the channel may be modified invarious manners, so as to modulate, e.g., increase, the sensitivity ofthe sensors, such as in the sensor array. Particularly, in variousinstances, it may be useful to configure the chamber and/or well so asto have a short channel length and a wide channel width, such as theshortest channel length and largest channel width possible, given theconfiguration of the one or more chambers in the one or more sensorarrays. More particularly, the equation for transconductance of thefield effect transistors disclosed herein is: g_(m)∝C_(ov) W/L V_(sd)where g_(m) is the transconductance, μ is the carrier mobility, C_(ov)is the overall capacitance of an included oxide or other layers over thetransistor, W is the channel width, L is the channel length and V_(sd)is the voltage from the source to the drain. Since g_(m) directlyrelates to the sensitivity of the sensor it is desirable to increaseg_(m) through the terms shown in the equation. In particular increasingthe W/L ratio (maximizing W and minimizing L) will increase g_(m).

In particular instances, the length of the channel from the source tothe drain ranges is less than 1 micron, such as less than 500 nm,including less than 50 nm, and in particular instances: as short as thefabrication process will allow without generating defects or resultsthat render the device unusable. In one particular implementation thechannel length may be 20 nm or less. Conversely, the width of thechannel may be as wide as feasible and/or possible. In such an instanceas this, the width of the channel need not be governed by thefabrication process as much as by the design requirements of the overallsensor chip. For instance, in specific instances, hundreds of thousandsto millions of sensors may be included in an exemplary sensor chip.

However, with such a large number of sensors, each individual sensorsize and/or pitch, e.g., which may directly affect the channel width,should be kept reasonably small so as to prevent the chip from being solarge as to be unable to be fabricated (e.g., such as exceeding thephotolithography reticle size) or too expensive (e.g., due to the effectof defect density on a large chip size). Hence, in one implementation,e.g., of a rectangular channel design, a practical range of the channelwidth may be from 0.1 micron to 2 microns. As indicated above, in someinstances, it may be desirable to increase the channel length to channelwidth ratio, such as through the use of various design techniques. Inone particular exemplary instance, a structure, such as aninterdigitated tooth and comb structure, can be provided such as forshort channel lengths and large channel widths, such as within arelatively compact area, such as shown in FIG. 11, which depicts variousdesigns of interdigitated source and drain electrodes that may beimplemented so as to increase the W/L of the channel within a relativelysmall area.

Another aspect of the present disclosure is the application of an ionsensitive layer to the channel to improve the sensitivity of the 1D or2D or 3D material of the field effect transistor. Hence, the 1D and/or2D layer may further be associated with an insulator material. Forinstance, the insulator material for the well structure may be anorganic material, such as a polyimide or BCB, and/or may be an inorganicmaterial, such as silicon oxide or silicon nitride. Alternatively, thechannel is composed of a silicene. Additional alternative materials forthe channel include borophene, WS2, boron nitride, stanene (2D tin),germanane, nickel HITP, and Mxenes (Ti2C, (Ti0.5, Nb0.5), V2C, Nb2C,Ti3C2, Ti3CN, Nb4C3 and Ta4C3), and the like.

In particular instances, a reaction layer may be provided, such as alayer associated with the 1D or 2D, e.g., graphene, layer. For instance,in one embodiment, a thin (0.01 micron) passivation or etch stop layermay be placed over the graphene layer, such as in the case where a welletch process affects the graphene layer. In various instances, an oxidelayer may be included, such as disposed within the chamber and/orchannel thereof. Particularly, in various embodiments, a method fordepositing the dielectric layer may include Atomic Layer Deposition(ALD). Another method for creating an analyte-sensitive layer may be tofirst deposit a metal layer (e.g., by sputtering or evaporation) ontothe 1D, 2D, or 3D material layer and then oxidizing the metal to form ametal oxide layer. It is further possible to combine material layersusing different deposition processes such as to create ananalyte-sensitive layer—for example a first layer may be comprised ofsputtered metal that is oxidized, followed by a layer comprised of anALD deposited oxide. It is also possible to combine two or moreanalyte-sensitive layers, such as comprised of different materials tocreate an overall analyte-sensitive layer stack. For example a firstlayer of metal, e.g., aluminum oxide, may be formed over the channelmaterial and then a second layer of metal, e.g., tantalum oxide, may beformed over the aluminum oxide. In some implementations ananalyte-sensitive dielectric layer need not be required nor used.

However, where employed, the oxide layer may be configured so as toprevent the nucleic acid template, e.g., present on a micro- ornano-bead, as presented herein, from contacting the 1D or 2D material orother reaction layer of the chamber directly. The oxide layer may becomposed of an aluminum oxide, tantalum oxide, and/or a silicon oxide.In various instances, the oxide layer may have a thickness of 9nanometers or less. In further instances, the chemically-sensitivefield-effect transistor can read through the oxide layer. In particularinstances, the well structure may include a permeable membraneassociated with the graphene layer.

In one aspect of the present disclosure is a chemically-sensitivetransistor, such as a field effect transistor (FET) that is fabricatedin a stacked configuration including a primary structure, such as awafer, e.g., a silicon wafer, as well as one or more additionalstructures. For instance, an insulator material layer may also beincluded on top of the primary structure, and may be an inorganicmaterial. The first and second structures may include a furtherstructure containing one or more of a conductive source and/or aconductive drain, such as separated one from another by a space, andembedded in the primary and/or secondary structures and/or may be planarwith a top surface of the secondary structure or a further layer orstructure associated therewith. In various instances, the structures mayfurther include a processor, such as for processing generated data, suchas sensor-derived data. Accordingly, the structures may be configuredas, or otherwise include, an integrated circuit, and/or may be an ASIC,a structured ASIC, or an FPGA.

For instance, as can be seen with respect to FIGS. 1A-1D, a graphenelayered substrate 10 for a chemically-sensitive field-effect transistor,such as for a system for the analysis of chemical and/or biologicalmaterials is provided. The substrate 10 includes a primary basestructure, such as composed of silicon. In various instances, thesilicon based primary structure 10 may be configured as a complementarymetal-oxide semiconductor (CMOS). The primary structure may include oneor more additional structures such as an insulator material layer 20.For example, the substrate may be in a stacked configuration such aswhere a secondary structure 10, e.g., including an insulator material20, is deposited or otherwise fabricated on top of the primary structure10.

The structured primary 10 and/or insulator layers 20 may further includea reaction layer 26. For instance, the stacked structured layers may beconfigured to include a further structure, such as a channel structure,which in turn may be adapted as the reaction layer 26. Particularly, incertain instances, the insulator layer 20 may include a channel 26, suchas containing one or more of a conductive source 22 and/or a conductivedrain 22, such as separated one from another by a space 26, and embeddedin the primary structure 10 and/or insulator material 20, and/or may beplanar with a top surface 21 of the insulator layer 20. The source 22and drain 24 may be composed of metal, such as damascene. In variousinstances, the insulator material for the channel structure 26 may be anorganic or an inorganic material. In a particular instance, the organicmaterial may be a polymer, polyimide, BCB or other like material. Inanother instance, the inorganic material may be a silicon oxide, e.g., asilicon dioxide, or a silicon nitride or other metal oxide or nitride.

In particular instances, the structures may be configured as acomplementary metal-oxide semiconductor (CMOS) 1, which in turn may beconfigured as a chemically-sensitive FET containing one or more of aconductive metal source 22, a conductive metal drain 24, a channel orother reaction zone 26, and/or a processor. For instance, the FET 1 mayinclude a CMOS structure having an integrated circuit that is fabricatedon a silicon wafer 10, which further includes a silicon dioxideinsulator layer 20, including a conductive damascene copper source 22and a conductive damascene copper drain 24, which may be embedded in atleast the insulator layer 20. In various instances, the structures mayinclude a surface 21, e.g., a top surface, which surface may include thechannel 26, such as where the surface and/or channel may be configuredas a reaction zone 26 that extends from the conductive source 22 to theconductive drain 24. An exemplary length of the surface and/or channel26 from the source to the drain may range from about 0.001 microns toabout 10 microns, such as from about 0.01 microns to about 5 microns,for instance, from about 0.05 micron to 3 microns, including about 0.1or about 0.5 microns to about 1 or about 1.5 or about 2 microns. Anexemplary width of the surface and/or channel from side to side mayrange from about 0.001 microns to about 10 microns, such as from about0.01 microns to about 5 microns, for instance, from about 0.05 micronsto 3 microns, including about 0.1 or 0.5 microns to about 1 or about 1.5or about 2 microns.

In certain instances, the surface and/or channel region may form areaction layer 26 that may include a material layer 30, which materiallayer may be a one-dimensional (1D) transistor material, atwo-dimensional (2D) transistor material, a three-dimensional (3D)transistor material, and/or the like. Accordingly, in various instances,a 1D transistor material may be included, which 1D material may becomposed of a carbon nanotube or a semiconductor nanowire. In otherinstances, a 2D transistor material may be included, which 2D materialmay include a graphene layer, silicene, molybdenum disulfide, blackphosphorous, and/or metal dichalcogenides. In various instances, a 3Dmaterial may also be provided.

For instance, in various embodiments, the material layer may be a singlelayer, 2D material, such as a graphene layer 30. Particularly, as can beseen with respect to FIG. 1B, graphene is a two-dimensional, monolayerof carbon atoms that are arranged as a lattice structure. This latticestructure forms regular hexagons with a carbon atom at each vertex. Insuch an instance, the bond length between adjacent carbon atoms may beabout 1.42 Å and the lattice constant may be about 2.46 Å. Thismolecular structure is very unique in that each carbon atom shares oneof its four free valence electrons with three of its adjacent and planarcarbon atoms such that each of the three planar carbon atoms isorientated at about a 120° with respect to the other three carbon atoms.Such an orientation gives graphene it's honeycomb, lattice structure.Additionally, the fourth valence electron forms a pi bond, perpendicularto the three planar signma-bonded carbon atoms, which is responsible forthe unique electronic characteristics of graphene.

Particularly, the single-layer, two-dimensional structure of graphenegives it at least three important characteristics with respect to itsuse herein: it creates the presence of a bandgap, it makes the graphenelayer a semimetal, and it promotes rapid charge transport (mobility andhigh-field transport) at room temperature. Hence, in various instances,a graphene FET, as herein described performs better as a biologicalsensor than a typical CMOS-FET device not having such a reaction layer.For instance, with respect to hybridization detection and/or sequencing,a traditional MOSFET transistor may have fundamental limitations in itssensitivity (due to channel thickness and intervening insulatinglayers), whereas the present gFET with its single atom thickness can beemployed to form a solution gated reaction zone and/or channel, whereinthe graphene layer may be in direct contact with the chemical reactionzone. Specifically, the reaction layers may include a 1D, 2D, and/or 3Dstructure 30 may be configured so as to have a much higher carriermobility than the typical doped silicon commonly used in MOSFET or ISFETdevices. This gives the herein disclosed 1D, 2D, and/or 3D FET sensordevices increased sensitivity to and faster detection of chemicalreactions. Further, in various instances, the surface and/or channel 26may include or make up a dielectric layer, such as for furtherincreasing sensor sensitivity and/or functioning.

Additionally, FIG. 1C depicts an alternative 2D material layer 30 thatmay be employed so as to increase sensitivity of the sensor so as tobetter enable the FET 1 to determine the presence and/or identity of oneor more reactants and/or products thereof that results from theoccurrence of a chemical and/or biological reaction that takes placeproximate a reaction zone 26 of the FET device. As can be seen withrespect to FIG. 1C, the 2D material layer in this instance is amolybdenum disulfide. Further 2D materials, as presented herein toincrease sensitivity of the sensors include a black phosphorous layer,as depicted in FIG. 1D, and silicone as depicted in FIG. 1E.Alternatively, a 1D material, such as a carbon nanotube may be employedfor these enhancement purposes, such as presented in FIG. 1F. Asemiconductor nanowire structure, as depicted in FIG. 1G may also beused.

In various instances, as can be seen with respect to FIG. 1H, a reactionlayer 34, e.g., an oxide layer, may be disposed on the surface and/orchannel 26, such as layered or otherwise deposited on the 1D, 2D, e.g.,graphene, or 3D layer 30. Such an oxide layer 34 may be an aluminumoxide or a silicon oxide, such as silicon dioxide. In some embodiments,the oxide layer may have a thickness of about 20 nanometers, such asabout 15 nanometers, such as 10 or 9 or 7 or 5 nanometers or less.Particularly, the oxide layer 34, when present, may be composed of analuminum oxide, a silicon oxide, a silicon dioxide, and the like.

In various instances, a passivation layer 36 may be disposed orotherwise be included on the surface and/or channel 26, such as layeredor otherwise deposited on the 1D, 2D, e.g., graphene, or 3D layer 30and/or on an associated reaction or oxidation layer 34 on the surfaceand/or channel 26. More particularly, the oxide and/or passivationlayers may have a suitable thickness such as of from about 100 nm orabout 75 nm to about 10 nm or 9 nm or less, such as about 0.5 microns orabout 0.1 microns or about 50 nanometers or less to about 20 nanometers,such as about 15 nanometers, such as about 7 or about 5 nanometers orless, respectively.

As can be seen with respect to FIG. 11, in particular instances, theprimary 10 and/or secondary 20 structures may be fabricated to includeor otherwise be associated with a tertiary structure 35, such as may becomprised of a silicon dioxide material. In various instances, thetertiary layer may be fabricated or otherwise configured so as toinclude a chamber or well assembly 38 in and/or on the surface 21. Forinstance, FIG. 11 depicts a field effect transistor in a stackedconfiguration and having a well structure 38, which well structure maybe positioned on a portion of a surface, e.g., an exterior surface,e.g., 21, of a primary 10 and/or secondary structures 20. In someinstances, the well structure 38 may have a plurality of walls orbounding members 39 a and 39 b set apart from each other by a distancethat may be coincident with the space 26 so as to form the verticalboundaries of the chamber 38, e.g., with the space 26 forming thehorizontal, bottom boundary. In particular instances, the horizontalsurface of the space 26 may be configured as a reaction zone so as toform a reaction region within the well 38. Particularly, boundaries 39 aand 39 b may be formed on top of, or may otherwise include at least aportion of the 1D, 2D, e.g., graphene, and/or 3D material 30, and/or mayadditionally include the reaction 34, e.g., oxide, and/or passivationlayers 36 (See FIG. 2B). In various instances, the chamber and/or wellstructure 38 may define an opening 37, such as an opening that allowsaccess, e.g., fluidic access, to an interior of the chamber 38, such asallowing direct contact with the 1D, e.g., carbon nanotube or nanowire,2D, e.g., graphene, or other 3D structure associated with the surfaceand/or channel 26.

Accordingly, as presented with respect to FIG. 2A, a further aspect ofthe present disclosure is a bio-sensor 1. The bio-sensor includes a CMOSstructure 10 that may include a metal containing source 22, e.g., adamascene copper source, as well as a metal containing drain 24, e.g., adamascene copper drain, such as embedded within an insulating and/ordielctric layer 20, e.g., positioned on top of the structure 10. Theinsulating layer may be an inorganic material, such as a silicon oxide,e.g., a silicon dioxide, or a silicon nitride, or an organic material,such as a polyimide, BCB, or other like material. The bio-sensor mayalso include a 1D or 2D or 3D layered, e.g., a graphene layered, surfaceor channel 26 extending horizontally from the source 22 to the drain 24,so as to at least be proximate therewith and thereby form a reactionzone 26.

In this instance, the surface structure 26 completely overlaps thesource 22 and drain 24 regions. A further layer of material 35 may bepositioned over the surface and/or channel region 26, which layer ofmaterial may further be etched or otherwise configured to include a wellor chamber structure 38 having a bottom surface that may be positionedon or proximate a portion of an exterior surface of the 1D or 2D or 3Dlayer, such as to be coincident with the channel region 26. In such aninstance, the well structure 38 may be a layered structure and mayinclude a plurality of surfaces, such as first 39 a and second 39 b wallstructures, such as extending from or otherwise being coincident withthe surface of the reaction zone 26. For instance, the wall structures29 a and 29 b may partially overlap the surface structure 26.Accordingly, FIG. 2A is an illustration of a chemically-sensitivefield-effect transistor having a graphene layered well structure 38,such as for a system for analysis of biological and/or chemicalmaterials.

In particular instances, the well structure 38 may be configured so asto define an opening 37 that allows for direct contact with the surface26, and thereby contact with the 1D, e.g., nanotube, nanowire, and/or2D, graphene, layer. Hence, in various embodiments, the cavitated FETdevice may be configured so as to include a plurality of graphene wellsor other chamber surfaces. In various instances, the FET device may beconfigured as a CMOS biosensor having a well structure 38 that furtherincludes an oxide and/or passivation layer 34, as shown in FIG. 2B,which passivation layer 34 may be disposed in or on one or more of thechamber surfaces 39. The CMOS structure 10 may additionally include thecomponentry typical of a CMOS semiconductor and/or transistor such asused and/or manufactured as a microchip. Hence, in certain instances, asillustrated in FIG. 2B, the CMOS field effect transistor 1 may beconfigured as a chemically-sensitive transistor, and may be adapted toinclude one or more structures, such as nano- or micro-wells 38, thatare formed as a reaction chamber, into which a solution, e.g., asolution containing one or more reactants, may be deposited, such as forthe performance of one or more biochemical reactions, such as a nucleicacid hybridization and/or sequencing reaction. In particular instances,the chamber 38 may include a layered surface 26 having a 1D, 2D, or 3Dmaterial, and/or one or more reaction 34 and/or passivation layers 36deposited therein. In such instances, the chamber of the CMOS device maybe configured as a solution gate and therefore the FET may be adapted soas to be an ISFET, such as configured for receiving the reactantsnecessary for performing an analysis of biological and/or chemicalmaterials, for instance, a hybridization and/or sequencing reaction.

In some embodiments, as can be seen with respect to FIGS. 2E and 2F, thechemically-sensitive field effect transistor 1 may include a pluralityof wells 38 a-38 e, having a plurality of openings 37 a-e, where eachwell 38 is associated with one or more sensors, and may thus beconfigured as an array, e.g., a sensor array. Such an array or arraysmay be employed to detect the presence and/or a change in concentrationof various analyte types, such as within the wells 38, in a wide varietyof chemical and/or biological processes, including DNA hybridizationand/or sequencing reactions. For instance, the devices herein describedand/or systems including the same may be employed in a method for theanalysis of biological or chemical materials, such as for whole genomeanalysis, genome typing analysis, micro-array analysis, panels analysis,exome analysis, micro-biome analysis, and/or clinical analysis, such ascancer analysis, NIPT analysis, and/or UCS analysis.

In a particular embodiment, a multiplicity of the wells 38 of thechemically-sensitive device may include a reaction zone 26 containing agraphene layer 30 so as to form a graphene FET (gFET) array 1. As hereindescribed, the gFET array 1 may be employed to facilitate DNA sequencingtechniques, such as based on monitoring changes in hydrogen ionconcentration (pH), changes in other analyte concentrations, and/orbinding events associated with chemical processes relating to DNAsynthesis and/or hybridization reactions, such as within the gatedreaction chamber or well 38 of the gFET based sensor 1. For example, thechemically-sensitive field effect transistor 1 may be configured as anarray of CMOS biosensors and/or may be adapted to increase themeasurement sensitivity and/or accuracy of the sensor(s) and/orassociated array(s), such as by including one or more surfaces 26 a-e orwells 38 a-e having a surface layered with a 1D and/or 2D and/or 3Dmaterial 30, such as graphene, a dielectric or reaction layer 34, apassivation layer 36, and the like.

For instance, in a particular embodiment, illustrated in FIGS. 2E and2F, a chemically-sensitive graphene field effect transistor (gFET) 1,such as a gFET having a CMOS structure is provided, where the gFETsensor, e.g., biosensor, may be configured as a microchip, having aplurality of wells 38 configured therein. In such an instance, themicrochip 1 may include a silicon base layer 10 within which the circuitcomponents of the transistor may be embedded. A dielectric layer 20,which may be a silicon dioxide layer, may be included, such as where thesilicon dioxide layer is embedded with a plurality of conductive sources22 a-e and conductive drains 24 a-e that are separated from one anotherso as to form a plurality of gate regions 26 a-e. In particularinstances, the gate regions are configured as a plurality of reactionzones 26 a-e, where each reaction zone may be contained within a wellstructure 38. In such an instance, the microchip 1 may include aplurality of gate regions 26 a-e that are configured as a plurality ofsolution gates 37 a-e.

Particularly, in various embodiments, each sensor of the plurality ofsensors includes a graphene field effect transistor. For instance, FIG.2C depicts a top plane view of a first embodiment of a field effecttransistor 1 having a channel structure 26 that is surrounded by a wellstructure 38, wherein a graphene layer 30 is deposited or otherwisepositioned over the channel structure 26. FIG. 2D depicts a top planeview of another embodiment of the field effect transistor 1 having achannel structure 26 that is surrounded by a well structure 38, whereinan oxide layer 34 is deposited or otherwise positioned over the graphenelayer 30, which in turn is positioned over the channel structure 26.Likewise, FIG. 2E depicts a top plan view of an array for a system foranalysis of biological or chemical materials. In various instances, thearray may include a plurality of sensors and one or more referenceelectrodes, such as a platinum or Ag/AGCl reference electrode. FIG. 2Fdepicts a portion of the wells of the array of FIG. 2E, in greaterdetail.

In various embodiments, one or more of the solution gates may include agraphene layered surface 30 a-e, which in various instances may furtherinclude one or more oxide 34 and/or passivation 36 layers, such aslayers that are disposed on the surface(s) of the bounding members ofthe wells or chambers 37 so as to increase the measurement sensitivityand/or accuracy of the sensors and/or associated array(s). Like above,in such instances, the solution gated chambers 37 of the arrays of theCMOS device may be configured as an ISFET, and be adapted for receivingthe reactants necessary for performing various analyses of biologicaland/or chemical materials, for instance, one or more hybridizationand/or sequencing reactions.

Accordingly, in one aspect, a system is provided, such as a systemconfigured for running one or more reactions on biological and/orchemical materials so as to detect a presence and/or concentrationchange of various analyte types in a wide variety of chemical and/orbiological processes. For instance, in some instances, the biologicalmaterial may be a nucleic acid or other biological molecule, such as aprotein, or the like. Hence, in particular instances, the system may beadapted for performing a DNA hybridization and/or sequencing reaction.In other instances, the analysis to be performed is for whole genomeanalysis, genome typing analysis, genomic panels, exome analysis,micro-biome analysis, and clinical analysis. In further analysisprocedures, one or more clinical analysis may be performed such as acancer analysis, NIPT analysis, and/or UCS analysis.

As such, the system may include an array 130 including one or more,e.g., a plurality of sensors, such as where each of the sensors includesor is otherwise associated with a chemically-sensitive field-effecttransistor having a conductive source, a conductive drain, and areaction surface or channel extending from the conductive source to theconductive drain. In particular instances, the array 130 may include oneor more wells configured as one or more reaction chambers having thereaction surface or channel positioned therein. In some instances, thesurface and/or channel of the chamber may include a one-dimensional(1D), or two-dimensional (2D), or three-dimensional (3D) transistormaterial, a dielectric or reaction layer, a passivation layer, and/orthe like.

As can be seen with respect to FIG. 3A, the system may include afluidics subsystem 100 for directing and controlling the flow of variousfluids throughout the system 1. The fluidics system 100 may in turninclude one or more of a fluidics component 120, such as for use inperforming the reaction, e.g., delivering one or more analyte containingsolutions to the array 130 for the performance of the reaction thereby,a circuitry component 140, such as for running the reaction and/ordetection processes, and/or a computing component 150, such as forcontrolling and/or processing the same. For instance, a fluidicscomponent 120 may be included where the fluidic component is configuredto control one or more flows of analytes and/or reagents over the array130 and/or one or more chambers thereof. Particularly, in variousembodiments, the system 100 includes a plurality of reaction locations,such as surfaces 26 _(a-n) and/or wells 35 _(a-n), which in turnincludes a plurality of sensors and/or a plurality of channels, andfurther includes one or more fluid sources 120, e.g., containing a fluidhaving a plurality of reagents and/or analytes therein, and fluidconduits, such as for delivery of the fluids from the source 120 to theone or more surfaces 26 and/or wells 35 of the array 130 for theperformance of one or more reactions thereby. In certain instances, amechanism for generating one or more electric and/or magnetic fields isalso included.

As can be seen with respect to FIG. 3B, the system 100 may additionallyinclude a circuitry component 140, such as where the circuitry componentmay include an address decoder 144, a sample and/or hold circuit 143, abias circuitry 142, and/or at least one analog-to-digital converter 141.For instance, the address decoder 144 may be configured to create acolumn and/or row address for each sensor of the array 130, such as byassociating a unique identifier with each sensor, such as based upon itslocation within a given row and column within the array 130. It may alsobe configured for inputting or otherwise directing the variousoperations that rely upon the addressing of operations for a given wellof the array. For instance, the address decoder 144 may target selectsignals to specific wells based on their column and/or row identifiers,so as to access a sensor and/or direct fluid flow to a given location,e.g., address within the array 130. The sample and hold circuit 143 maybe configured to hold an analog value of a voltage to be applied to oron a selected well or column and/or row line of an array 130 of a deviceof the disclosure, such as during a read interval. Likewise, the biascircuitry 142 may be coupled to one or more surfaces and/or chambers ofthe array 130 and may include a biasing component such as may be adaptedto apply a read and/or bias voltage to selected chemically-sensitivefield-effect transistors of the array 130, e.g., such as to a gateterminal of the transistor. The analog to digital converter 141 may beconfigured to convert an analog value to a digital value 142, forinstance, as a result and/or output of the reaction within an identifiedwell 35 or selection of wells, e.g., a line of columns and rows.

Additionally, as can be seen with respect to FIG. 3C, a computingcomponent 150 may also be included, such as where the computingcomponent 150 may include one or more processors, such as a signalprocessor 151, a base calling module 52, and an analytics module 153.The signal processor 151 may be configured for determining one or morebases of one or more reads of a sequenced nucleic acid, such as resultsfrom a sequencing reaction. The base caller of the base calling module152 may be configured to correct a plurality of signals, such as forphase and signal loss, to normalize to a key, and/or to a generate aplurality of corrected base calls for each flow in each sensor toproduce a plurality of sequencing reads. The analytics module 153 may beconfigured for performing one or more analytics functions on thesequenced data, and may include one or more of a mapping module,configured for generating one or more seeds from the one or more readsof sequenced data and for performing a mapping function on the one ormore seeds and/or reads; an alignment module, configured for performingan alignment function on the one or more mapped reads; a sorting module,configured for performing a sorting function on the one or more mappedand/or aligned reads; and/or an variant calling module, configured forperforming a variant call function on the one or more mapped, aligned,and/or sorted reads. In various embodiments, the device and/or systemmay include at least one reference electrode.

Particularly, the system may be configured for performing a sequencingreaction. In such an instance, the device for performing the sequencingreaction may be adapted from a complementary metal-oxide semiconductorreformed to include one or more reaction chambers, e.g., micro ornano-wells, so as to form an array 130. The array 130 may be associatedwith one or more sensors having one or more chemically-sensitivefield-effect transistors linked therewith. Such transistors may includea cascode transistor having one or more of a source terminal, a drainterminal, and or a gate terminal, such as forming a reaction zone. Insuch an instance, the source terminal of the transistor may be directlyor indirectly connected to the drain terminal of the FET. In someinstances, the gate terminal may be or may otherwise include a channelconfiguration, and may further include a one or two dimensional materialassociated with the gate. The 1D or 2D material may extend from thesource terminal to the drain terminal, such as where the 1D channelmaterial may be a carbon nanotube or nanowire, and the 2D channelmaterial may be composed of graphene, silicene, a phosphorene, amolybdenum disulfide, and a metal dichalcogenide. The device may furtherbe configured to include a plurality of arrays, such as arranged as oneor more lines of columns and rows coupled to the sensors in the array ofsensors. In such an instance, each column line in the plurality ofcolumn lines may be directly or indirectly connected to or otherwise becoupled with the drain terminals of the transistors, e.g., cascodetransistors, of a corresponding plurality of sensors or pixels in thearray, and likewise each row line in the plurality of row lines may bedirectly or indirectly connected to or otherwise coupled with the sourceterminals of the transistors, e.g., cascode transistors, of acorresponding plurality of sensors in the array.

In some instances, a plurality of source and drain terminals having aplurality of reaction surfaces, and/or associated channel members,extended there between may be included, such as where each channelmember includes a one or two dimensional material. In such an instance,a plurality of first and/or second conductive lines may be coupled tothe first and second source/drain terminals of the chemically-sensitivefield-effect transistors in respective columns and rows in the array.Additionally, control circuitry 140 may be provided and coupled to theplurality of column and row lines such as for reading a selected sensorconnected to a selected column line and/or a selected row line. Thecircuitry may also include a biasing component 142 such as may beconfigured for applying a read voltage to the selected row line, and/orto apply a bias voltage such as to the gate terminal of a transistor,such as FET and/or cascode transistor of the selected sensor. In aparticular embodiment, the bias circuitry 142 may be coupled to one ormore chambers of the array 130 and be configured to apply a read bias toselected chemically-sensitive field-effect transistors via theconductive column and/or row lines. Particularly, the bias circuitry 142may be configured to apply a read voltage to the selected row line,and/or to apply a bias voltage to the gate terminal of the transistor,e.g., cascode transistor, such as during a read interval.

A sense circuitry may be included and coupled to the array so as tosense a charge coupled to one or more of the gate configurations of aselected chemically-sensitive field-effect transistor. Sense circuitrymay also be configured to read the selected sensor based on a sampledvoltage level on the selected row and/or column line. In such aninstance, the sense circuitry may include one or more of a pre-chargecircuit, such as to pre-charge the selected column line to a pre-chargevoltage level prior to the read interval; and a sample circuit such asto sample a voltage level at the drain terminal of the selectedtransistor, e.g., cascode transistor, such as during the read interval.The sample circuit may also be included and contain a sample and holdcircuit 143 configured to hold an analog value of a voltage on theselected column line during the read interval, and may further includean analog to digital converter 141 to convert the analog value to adigital value.

In a further aspect, as seen with respect to FIG. 8A, a biologically andchemically-sensitive FET sensor 1 is provided wherein the sensorincludes a stacked configuration having a plurality of layers and/orstructures therein. For instance, a primary structure 10 includes aninorganic base layer, e.g., a silicon layer, which is fabricated tocontain or may otherwise be configured as a CMOS FET. Accordingly,stacked on top of the base layer 10 may be a secondary structure 20 thatmay be configured as a dielectric layer and/or another inorganic ororganic insulator layer, such as a silicon dioxide layer. The primary 10and/or secondary 20 structures may additionally include or otherwise beconfigured to contain a conductive source 22 and drain 24 embedded inone or more of the structured layers, such as between and/or forming agate structure 26. In particular embodiments, an additional structure orlayer 35 may be positioned above the primary and secondary layers, whichlayer 35 may be etched to form one or more well structures 38, whichwell structure may be coincident with and/or proximate to the gatestructure 26 so as to form a solution gate region therewith. In variousembodiments, the solution gate region may include or otherwise be formedby the gate structured layer 26 as well as the bounding wall members 39a and 39 b forming the well structure 38, such as by extending laterallyupwards from the surface 21 and/or structured layer 26, and havingopening 37 positioned therein so as to access the gate region 26.

The well structure 38 may further include one or more additionalstructures and/or layers, such as a 1D or 2D or 3D material 30 and/or anoxidation 34 and/or passivation 36 layers that may be positioned betweenthe conductive source 22 and drain 24 and/or between wall members 39 aand 39 b in such a manner as to form a bottom surface and/or reactionzone 26 of the chamber 37. In various instances, one or more of thestructures may further include or otherwise be associated with anintegrated circuit and/or a processor, such as for generating and/orprocessing generated data, such as sensor derived data, e.g. indicativeof a sequencing and/or hybridization reaction taking place within thewell structure 38. In particular embodiments, a further structured layer40, e.g., a secondary or tertiary or quartier structure, may also beprovided, such as where the further structured layer may be includedand/or present on a surface 26 or otherwise within the well or chamber37, such as to enhance the ability of the sensor and/or the processor todetermine the difference between a current and/or voltage applied acrossthe source 22 and/or drain 24 of the transistor, as well as theirrespective associated charge curves, as described herein.

For instance, in the exemplary embodiment of FIG. 8A, a biologicallyand/or chemically-sensitive field-effect transistor 1 having a graphenelayered 30 well structure 37 containing a further structured layer 40configured for enhancing the sensitivity of an associated sensor. Inthis embodiment, the structured well layer 40 is configured as apermeable membrane that may be associated with the graphene 30 and/orreaction 34 layers. Particularly, the chemically-sensitive FET sensor 1includes a surface 21, which surface may be within a well chamber 37,and be configured as a reaction region 26. The surface 21 of thereaction region 26 may be coupled to or otherwise include a 1D or 2Dmaterial such as a graphene layer 30 for detecting the presence of oneor more chemical and/or biological events and/or elements resultingthereby. Accordingly, the surface 21 may be configured as a reactionregion 26, and the well chamber 37 may be adapted such that a chemicaland/or biological reaction may take place therein. The surface 26 and/orgraphene structured layer 30 may be coupled with or otherwise include anadditional structure, such as the permeable membrane 40, that isconfigured to enhance the ability of the graphene-based sensor 1 todetect the presence of a chemical and/or biological reaction.Particularly, the additional structure 40 may be an ion-selectivepermeable membrane that is positioned proximate to and/or over areaction zone 26, which may be configured as a channel, and whichmembrane 40 may be adapted such that it only allows ions of interest totravel through the membrane 40, while excluding those ions that mightcause interference with the sensing capabilities of the sensor 1.

For example, in particular instances, the membrane material 40 may be anorganic or an inorganic material. A suitable membrane may be aninorganic material such as an oxide. An alternative material may be aseparate layer, such as an additional 1D or 2D material, e.g., ofgraphene, which is not electrically connected to the FET or itscomponent parts, e.g., the source 22 and drain 24. Another alternativematerial may be a polymer, such as Nafion, PEEK, a perfluorosulphonic,and/or a perfluorocarboxylic material. Alternatively, the material maybe a HMDS or other siloxane, such as positioned under a graphene layer30. Yet another alternative may be a getter material, such as containinga positive ion, e.g., NA⁺, which may be positioned within the chamber37, or may be positioned elsewhere on the sensor, such as a wall 39 aand/or 39 b thereof, and/or in a package that is adapted to attractunwanted ions. In another embodiment, the sensor enhancement material 40may be an ion-selective functional layer(s) that is positioned over thesensor and adapted so as to detect contaminants, unwanted ions, or otherimpurities that may react with the reactants within the well 38 suchthat their interactions with the sensor 1 and thus the variousdeterminations that the sensor 1 makes with respect to the reactionstaking place therein, such as in relation to detecting the presence orabsence of a desired ion, can be filtered out.

Accordingly, the chemically-sensitive field-effect transistors, aspresented herein, for a system for analysis of biological and/orchemical materials, may be configured as solution gated field effecttransistor devices having rows and columns of reaction chambers formedtherein. In various instances, the field-effect transistors comprise astructure having or otherwise being associated with a channel and aprocessor. In such instances, the structure may include one or more ofan insulating structure, a conductive source, a conductive drain, and/ora channel extending from the conductive source to the conductive drain,such as where the source and drain are embedded in the insulator and maybe positioned therein so as to be planar with a top surface of theinsulator. As indicated, in certain embodiments, the source and drainmay each composed of a damascene copper material. Further, the channelmay be composed of a one dimensional transistor material or atwo-dimensional transistor material. And where desired, a reaction layermay be associated with the graphene layer, and in some instances, mayinclude a passivation layer or etch stop layer that may be placed overthe channel, such as between the two layers and/or above the graphenelayer.

As can be seen with respect to FIGS. 4A-4C, in various instances, achemically-sensitive field-effect transistor 1 having a graphene layeredmicro- or nano-well structure 38 is provided. The FET 1 is configured asa microchip that includes a substrate layer 10 and an insulating layer20 within which is embedded the various transistor components includinga conductive source 22 and conductive drain 24 which may be adapted toform a gate region 26. In this instance, a graphene layer 30 may bepositioned over the insulating layer 20 and positioned so as to contactat least a proximate portion of the source 22 and a proximate portion ofthe drain 24. In this instance, the substrate layer 10 is composed ofsilicon, the insulating layer 20 is composed of silicon dioxoide, andthe source 22 and drain 24 are composed of a conductive metal, such ascopper.

The source 22 and the drain 24 are separated from one another andpositioned relative to the graphene layer 30 so as to form a gatestructure 26. In this embodiment, the gate structure 26 is furtherbounded by chamber walls 29 a and 29 b, which together form the well 28into which a fluid may be delivered, such as for the performance of abio-chemical reaction, and thus, forming a solution gate configuration.Particularly, an additional layer 35, which may also be composed ofsilicon dioxide, may be positioned above the first silicon dioxide layer20, and be configured, e.g., via micro etching, to form a micro- ornano-well 38 so as to form a chamber 37, which chamber 37 may be adaptedto receive a solution so as to form the solution gate region. Thegraphene layer 30 is disposed between the first 20 and second 35 silicondioxide layers such as to form the bottom surface of the chamber 37. Inthis instance, the FET sensor is configured to detect a change in ionconcentration, e.g., pH, which occurs within the well 38 such as when asolution containing reactants is added to the gate region within thechamber 37, and the reactants interact with an additional elementcontained within the chamber, such as a bound nucleic acid template.

Particularly, one or more solutions may be added to the chamber 37, suchas in the performance of a bio-chemical reaction. For instance, a firstsolution including a nano- or micro-bead 60 may be added to the well 38.The nano- or micro-bead may be treated so as to be associated with oneor more biopolymers, such as a DNA and/or RNA template 65. Once thenano- or micro-bead containing solution is added to the well 38, in sucha manner that the bead 65 is retained therein, one or more additionalsolutions containing reactants, such as for the performance of abiological and/or chemical reaction, may then be added to the well 38.For example, where the biological and/or chemical reaction is anucleotide synthesis reaction, the analyte containing solution to beadded to the well 38 may include a nucleotide and/or polymerasecomposition that if the conditions are suitable within the chamber 37will result in a binding event occurring between the template molecule65 and the nucleotide reactant, thus resulting in the reaction takingplace. Additionally, where the biological and/or chemical reaction is ahybridization reaction, the bound template molecule 65 may be configuredas a probe, and the analyte containing solution to be added to the well38 may include an additional DNA/RNA molecule of interest, which if theconditions within the chamber 37 are suitable will hybridize to thebound probe, thus resulting in the reaction taking place.

In either instance, the sensor 1 may be configured for detecting theoccurrence of a reaction event taking place, such as by detecting achange in the ionic concentration within the solution within the chamber37. Particularly, if the conditions are suitable for a reaction to takeplace, e.g., the appropriate reactants are present, a binding event willoccur in such a manner that an ion, such as an H⁺ ion, will be releasedinto solution, such as within the chamber 37 and/or proximate thesolution gate 26. In such an instance, the sensor 1 may be configured tosense the evolution of the ion, appreciate the change in pH, and detectthat a reaction has taken place. In such a manner as this, a DNA/RNAmolecule may be synthesized and/or a hybridization event determined.

Accordingly, as illustrated with respect to FIG. 4A, achemically-sensitive field-effect transistor 1 is provided wherein thetransistor 1 includes a graphene layered well structure 38 containing anano- or micro-bead 60 therein, such as where the graphene layer 30 maybe coincident with a channel region 26 so as to form a reaction zonetherewith. Further, in various instances, such as illustrated in FIG.4B, in addition to a graphene layer 30, the reaction zone 26 within thechamber 37 of the well 38 of the transistor 1 may further include areaction layer 34, such as a reaction layer, e.g., an oxide layer,associated with the graphene layer 30. In addition to the reaction layer34, the reaction zone 26 may additionally include a passivation or ESLlayer 36. Furthermore, as can be seen with respect to FIG. 4C, incertain embodiments, the chemically-sensitive field-effect transistor 1may include a plurality of nano- or micro-beads therein, such as withinthe chamber 37 of the well 38 of transistor 1, so as to allow aplurality of reactions to take place at the same time involving aplurality of substrates, 60 a and 60 b, within the well, which increasesthe surface area for reactions.

In some instances, it may be useful to provide a mechanism for assistingthe targeting of the microbead(s) 60 to the reaction zone 26 of the FET1. Particularly, as can be seen with respect to FIGS. 5A-E, achemically-sensitive field-effect transistor 1 is provided. In thisinstance, the transistor 1 may be a multi-layered structure including aprimary, e.g., a substrate layer 10, a secondary structure layer, e.g.,an insulator layer 20, and may further include an additional layer 35,e.g. a silicon dioxide layer, which layer may be cavitated so as toinclude a divot 38, such as a divot on a surface 21 of the substrate,and sized to at least partially contain a nano- or micro-bead 60therein. In certain instances, the surface of the divot 38 may becentered such that the bead 60 rests within the divot 38 so as to beproximate the reaction zone 26 and/or a channel structure associatedtherewith. In particular instances, the reaction zone 26 includes agraphene layer 30 positioned at least partially between the primary andtertiary layers, and in such instances, a silicon dioxide layer 34 maybe positioned above the graphene layer within the reaction zone 26. Inthis instance, to draw and/or attach the bead(s) 60 to the reaction zone26, an electromagnetic field may be employed. Hence, as shown in FIG.5A, a microbead 60 is positioned on the transistor surface 21, withinthe reaction zone 26, and in proximity to a channel.

More particularly, the reaction zone 26 of the FET 1 may be configuredto include a channel region that is formed to correspond to the region,e.g., point, of contact between the surface of the graphene layer 30 andthe bead 60. Further, to facilitate this contact, the FET 1 may includean attracting mechanism 70 that is configured to attract or otherwisedraw the bead 60 in to proximity of the reaction zone and/or channel 26.For instance, in particular instances, the nano- or micro-bead 60 mayinclude a charged and/or metallic element, and the attracting mechanism70 may be configured so as to generate an electric and/or magneticfield, such as for drawing the bead 60 to the reaction zone 26. Forexample, in some embodiments, the electric field generator 70 may be apulse generator, and in other embodiments, such as illustrated in FIG.5A, the magnetic field generator 70 may be a magnet.

Particularly, as shown in FIG. 5A, one or more nano- or micro-bead 60 ofthe disclosure may be configured for facilitating the performance of abio-chemical reaction such as on a reaction surface 26 of the sensordevice 1. For instance, in particular embodiments, each of the one ormore microbeads may include a biological material or a chemicalmaterial, associated therewith. In such an instance, the bead 60 may beintroduced to the surface 26 of the sensor device 1 of the system, suchas for nucleic acid sequencing, in such a manner that it is drawn orotherwise attracted to the surface 26, such as by electro-magnetism. Forinstance, the bead 60 may be configured to include electric chargeand/or paramagnetic properties so as to assist it in being drawn intoproximity of a reaction location 26 positioned on a surface 21 of thedevice 1, such as where the nucleic acid sequencing reaction may takeplace. Hence, the device may include an electro-magnetic fieldgenerating component 70 that is configured to apply an electro-magneticfield that is focused within the reaction zone 26 so as to interact withthe electric charge and/or paramagnetic properties of the bead 60thereby drawing it into proximity of the surface 21 and/or in to thereaction zone 26, such as via electro-magnetism. In this instance, thelayers and other components of the sensor device 1 are configured insuch a manner that the reaction zone 26 need not include boundingmembers, or if included the bounding members may be thin, allowing for ahigher density of wells on the array.

Alternatively, in other embodiments, such as presented in FIG. 5B, thebio-chemical sensor device 1 may include a well structure 38 that isconfigured for receiving one or more nano- or micro-beads, such as fornucleic acid sequencing therein. For instance, each of the one or moremicrobeads includes an analyte and/or reactant, which is configured forparticipating in a reaction, such as a nucleic acid hybridization and/orsequencing reaction. Accordingly, the sensor device 1 may include areaction location 26 that may be configured as a surface within a well38 of the device 1, such as where the reaction location 26 is proximatea channel and/or sensor of the device 1. The nano- or micro-bead 60 maybe configured for use in a system for analysis of biological and/orchemical materials such as on or within a reaction surface 26, such aswithin a well 38 of the sensor device 1. In this and other instances,the bead 60 may be introduced to the surface 26 of the sensor device 1of the system in such a manner that it is drawn or otherwise attractedtoward the reaction surface 26, e.g., of a well structure 38, where thenucleic acid sequencing reaction may take place, such as byelectro-magnetism.

For example, the bead 60 may be configured to have an electric chargeproperty and the bead attracting mechanism 60 may be configured to emitan electric field that is opposite in nature to the charge on the beadand is thereby adapted for draw the bead 60 into proximity of thereaction surface 26. In such an instance, an electric field componentgenerates an electric field to interact with the electric chargeproperties of the microbead. Hence, the microbead may be drawn to thereaction location using electrophoresis. In other instances, the bead 60may be configured to include paramagnetic properties so as to assist itin being drawn or otherwise attracted toward reaction surface 26, e.g.,into the well 38, and into proximity of the reaction zone, where thereaction may take place. The device, therefore, may include a magneticfield generating component 70 that is configured to apply anelectro-magnetic field that is focused within the chamber 38 so as tointeract with the paramagnetic properties of the bead 60 thereby drawingit into the chamber 38 and/or proximate the reaction surface 26, such asvia magnetism. Particularly, in various embodiments, the bead attractingmechanism 60 may be configured to emit a magnetic field that is oppositein polarity to the paramagnetic properties of the bead and is therebyadapted for draw the bead 60 into proximity of the reaction surface 26.In such an instance, a magnetic field component generates a magneticfield to interact with the polar properties of the microbead. The use ofmagnetism and/or electrophoresis allows for thinner reaction locationstructures.

Additionally, as illustrated in FIG. 5B, in some embodiments, the systemand its components may be configured such that when the electro-magneticfield is generated it interacts with the bead 60 and/or a componentassociated therewith so as to pull the bead toward the reaction zone 26.In other embodiments, as illustrated in FIG. 5C, the system and itscomponents may be configured such that when the electro-magnetic fieldis generated it interacts with the components of the bead 60 so as topush the bead away from the reaction zone 26. Accordingly, theelectromagnetic fields can be generated and/or reversed so as to attractor repulse the nano-/micro-bead to or from the reaction location 26,such as to or away from a well 38, and thus utilizing an electronicand/or magnetic field, the nano- or micro-bead may be positioned withinthe device, such as within a well thereof.

As illustrated in FIG. 5D a chemically-sensitive field-effect transistor1 is provided, such as for a system for analysis of biological and/orchemical materials, such as by utilizing an electric and/or magneticfield generating mechanism such as for positioning of a nano- ormicro-bead 60 in relation to the reaction surface 26. For instance, inparticular instances, a voltage may be applied between a location abovethe solution of the solution gate 37 and a location on or below thereaction location 26, such as above the package lid 72 and/or below ametal component, e.g., a plate, below the package 72. In certaininstances, the location below the reaction location 26 may include ametal or other conductive layer such as within the package or packagesubstrate. Hence, in various instances, the field generating mechanism70 may be employed to generate and/or reverse an electric or magneticfield so as to insert or eject one or more beads from one or more wells,sensors, and/or channels associated therewith, either entirely orselectively.

Particularly, as set forth in FIG. 5E, an array 1 ofchemically-sensitive field-effect transistors for a system for analysisof biological or chemical materials is provided. The array 1 includes amultiplicity of wells 38 a-e each forming a reaction location 26 a-ewhereon a bio-chemical reaction may take place. Additionally, eachreaction location 26 is associated with a field generator 70 a-e, e.g.,a magnet, which is configured so as allow for the selective filling ofthe reaction locations 26 with one or more types of nano- or microbeads60 a-e. Accordingly, by utilizing multiple field generators 70 a-70 e,e.g., multiple magnets, for generating a plurality of electro-magneticfields, the nano- or micro-beads 60 a-e may be positioned within theplurality wells 38 a-e. Such positioning may be selective such as byselecting which generators will be on, off, or reversed, so as to fillor not fill their respective wells 38 a-e, as desired. In variousembodiments, the electromagnetic fields for any given well 38 may bereversed so as to expel a bead 60 from the well 38 and/or reaction zone26.

Particularly, in a further aspect of the present disclosure, a systemhaving an array of chemically-sensitive transistors, such as fieldeffect transistors (FET) including a plurality of chambers 37 a-e havingwell structures formed therein is provided. In such an instance, thewells 38 a-e may be structured as or may otherwise include reactionlocations, 26 a-e, wherein one or more chemical reactions may takeplace. In such an embodiment, the system may include one or morefluidics components having one or more fluid sources, e.g., reservoirs,containing one or more fluids therein and configured for delivering thefluid from the reservoir to the reaction chamber, such as for thedetection of a biologic and/or the performance of one or more chemicaland/or biological reactions, such as a nucleic acid sequencing reaction.Accordingly, the fluidics component, e.g., the fluid source, may be influidic communication with the FET device configured for biologicaland/or chemical analysis, and may be configured for controlling a flowof reagents over the array.

Accordingly, in certain instances, the fluid may include one or morereactants, such as one or more analytes necessary for performing asequencing reaction, as herein described. In a particular embodiment,the fluid may include one or more, e.g., a plurality of microbeads 60,having a nucleic acid template 65 attached thereto, for instance, wherethe template is a DNA or RNA molecule to be sequenced, and the fluidcontaining the microbead 60 is to be delivered to the well 38 such asfor carrying out the sequencing reaction. In such an embodiment, one ormore of, e.g., each, of the plurality of microbeads may be configured soas to have electric charge and/or paramagnetic properties. The devicemay additionally include an electric and/or magnetic field component,e.g., having an electric and/or magnetic field generator, such as wherethe electric and/or magnetic field component is configured to generatean electric and/or magnetic field so as to interact with the electricand/or magnetic charge properties of each of the plurality of microbeadsto attract the microbeads into a reaction location, such as a reactionsurface, a channel, a well, a chamber, and/or a sensor of the FETdevice, such as by using electrophoresis and/or magnetism.

Hence, one or more, e.g., a plurality of microbeads 60 a-e, may be drawnonto or into a reaction location of the plurality of reaction locations37 a-e, which locations may be formed as wells, e.g., one or more thinwells. The use of magnetism or electrophoresis allows for thinnerreaction location structures. In particular instances, electric and/ormagnetic field generator may be configured for drawing and/orpositioning the microbeads within the well structure 37, such as inproximity to a channel or chamber of the device, and in other instances,the electric and/or magnetic field generator may be configured forreversing the electrical and/or magnetic field so as to repulse themicrobead(s) 60 from the reaction location, channel, and/or chamber 37.In various instances, an array of reaction locations may be providedeach having a magnet 70 a-e that allows for selective filling of thereaction locations with different numbers and/or types of microbeads 60,such as at select reaction locations 37 a-e. In such an instance,multiple electric and/or magnetic field generators for selective fillingof reaction locations, e.g., wells.

Accordingly, one aspect of the present disclosure is a system and/or amethod for positioning one or more, e.g., a plurality, of microbeads 60within a reaction or plurality of reaction locations 37 for biologicalor chemical analysis, such as for nucleic acid sequencing. The systemmay include a CMOS FET device having an integrated circuit structureconfigured for performing a biological or chemical analysis, such aswithin a plurality of nano- or micro-reaction wells, as described above,having a fluidic component 120, a circuitry component 140, and/or acomputing component 150, and the method may include one or more of thefollowing steps. For instance, the method may include the fluidiccomponent 120 introducing a fluid to be in contact with the device 1,such as where the fluidics component is configured to control a flow afluid of reagents over the array 1, and the fluid may include one ormore microbeads 60 that may have electric charge and/or paramagneticproperties. In such an instance, the device may include an integratedcircuit structure, a plurality of reaction locations 37 having one ormore wells, a plurality of sensors and/or a plurality of channels,and/or an electric and/or magnetic field component 70. The electricfield and/or magnetic field component 70 may be configured to activatethe electronic and/or magnetic field, and the method may also includeactivating an electric and/or magnetic field so as to interact with theelectric and/or paramagnetic properties of each of the microbeads 60.The method may additionally include drawing the one or more microbeads60 into proximity with a reaction zone 26 of the plurality of reactionlocations 37 using electrophoresis and/or magnetism. In certaininstances, the method may include positioning the one or more microbeadswithin the one or more reaction locations for biological or chemicalanalysis.

In particular instances, the electric and/or magnetic fields may begenerated by the plurality of electric and/or magnetic field generators70, e.g., included in the integrated circuit structure, in all or only asubset of the plurality of reaction locations 37 so as to only attract aplurality of microbeads 60 to the subset of reaction locations, such asfor selectively filling the plurality of reaction locations 37 with theplurality of microbeads. In such an instance, different types ofmicrobeads may be attracted to different reaction locations, such as bypulsing the voltage and/or magnetic generators and/or keeping the sameconstant. Particularly, where an electric field generator 70 is providedthe voltage applied to the device 1 may be variable or constant and maybe less than about 10V, such as about less than 8V, or less than about6V, including less than about 4V or about 2V or 1V. The voltage may beapplied between a location above the fluid 72 and a location on or belowthe reaction zone 26, such as above the package lid and/or below themetal plate below the package. In certain instances, the location belowthe reaction location may be a metal or conductive layer such as withinthe package or package substrate. The method may also include the stepof reversing the electric or magnetic field so as to eject the pluralityof beads from the plurality of wells, sensors, and/or channels, eitherentirely or selectively.

Further, as indicated, each or a subset of the plurality of reactionlocations may be utilized to generate electric fields to attract amicrobead thereby allowing for programmability to each or a subset ofreaction locations, for instance, 99% or 95% or 90% or 85%, or 80% orless of the plurality of wells are occupied with a microbead. Hence, theelectric and/or magnetic field may be generated in only a subset of theplurality of wells 38 a-e, sensors or channels to only attract aplurality of microbeads 60 a-e to the subset. Likewise, a plurality ofelectric and/or magnetic field generators 70 a-e for selective fillingthe plurality of wells 38, sensors or channels with the plurality ofmicrobeads, and/or ejecting the plurality of beads 60 from the pluralityof wells 38, sensors or channels. In such an instance, the electricand/or magnetic field generator may be an electric source, a permanentmagnet and/or an electromagnet. As indicated, the plurality of magneticfield generators is configured to reverse the magnetic field to ejectthe plurality of microbeads 60 from the plurality of reaction locations37 or a subset thereof.

Additionally, in one aspect of the present disclosure, a device, system,and/or method for verifying well occupancy for a plurality of wells 38a-e for analysis of biological or chemical materials may be provided.The system may include a device for receiving a fluid containing theplurality of microbeads 60. Particularly, the device may include aprocessor, a CMOS structure having an integrated circuit, a plurality ofwells 38, and a plurality of sensors within the CMOS structure. Each ofplurality of wells 38 may be configured to receive a microbead 60 of theplurality of microbeads, and the CMOS structure may include a mechanism70 for drawing and/or ejecting the beads into or out of the wells.Hence, the method may include the step of flowing the plurality ofmicrobeads 60 over and/or into the plurality of reaction locations 26/37and/or wells 38 and/or may include determining, e.g., through electricaland/or magnetic sensing if a reaction location 26/37 and/or well 38 isoccupied or unoccupied and/or if a location 26/37 contains one ormultiple microbeads 60.

Consequently, the processor 140 may be configured to determine if a wellis unoccupied and/or if the well contains one or more, e.g., multiplemicrobeads. In certain instances, the processor 140 may also beconfigured to eliminate or modify one or more of the measurements, suchas based on the number of wells occupied or unoccupied, e.g., the numberof wells containing none, one or multiple microbeads. For instance, theprocessor 140 may be configured to eliminate from the measurement thenumber of wells unoccupied and the number of wells containing multiplemicrobeads, or compensate in the measurement for the number of wellsunoccupied and the number of wells containing multiple microbeads, andthe like. In such instances, the measurement may be a shift in an I-V orI-Vg curve, as explained below. In particular instances, the processor140 may be configured to eliminate from the measurement the number ofwells unoccupied and the number of wells containing one or multiplemicrobeads and/or to compensate in the measurement for the number ofwells unoccupied and the number of wells containing one or multiplemicrobeads. Accordingly, in some embodiments, the measurement may be ashift in an I-V or I-Vg curve, such as one or more of: generating aplurality of I-V or I-Vg curves so as to determine a shift in responseto a chemical reaction occurring on or near the chemically-sensitivefield effect transistor; generating a chemically-sensitive field-effecttransistor I-V or I-Vg curve in response to a chemical reactionoccurring on or near the chemically-sensitive field-effect transistor soas to detect a change in the slope of the I-V curve; and/or to senseshifts in a capacitance as a function of a gate voltage.

As indicated above, in particular embodiments, the field effecttransistor may be configured as a complementary oxide semiconductor thatis further adapted so as to be cavitated, so as to include one or morereaction chambers that are positioned so as to align with a gate regionof the FET. In such instances, the FET may be in contact with a fluidicsource so as to form an ISFET. Accordingly, the CMOS-ISFET may beconfigured to run one or more chemical and/or biological reactionswithin its various chambers, such as a DNA sequencing reaction, and thelike, such as proximate a solution gated reaction zone. For thesepurposes, the ISFET may include a processor configured for controllingthe performance of the one or more reactions, e.g., involving abiological or chemical material, so as to obtain reaction results, andfor analyzing those results, for instance, based on detecting and/ormeasuring changes in a voltage (V) potential, current (I), orcapacitance occurring within the gate region on the chemically-sensitivefield effect transistor.

Particularly, as can be seen with respect to FIG. 6A, the processor,such as a signal processor 151, may be configured so as to generate oneor more current (I) vs. voltage (V) curves, such as where the current Iof the I-V curve is the current applied between the source 22 and drain24 of the chemically sensitive solution gated field effect transistorand/or where the gate voltage (Vg) of the I-Vg curve is a gate 26/37voltage applied to the chemically-sensitive field effect transistor 1.In such an instance, the gate voltage Vg of the I-Vg curve may be a topand/or a back gate voltage that may be applied to the chemicallysensitive field effect transistor 1 through a top (or front) and/or backof the device, respectively. In particular embodiments, the gate voltageVg of the I-Vg curve may be a solution gate voltage such as applied tothe chemically sensitive field effect transistor through a solutionflowed over a portion, e.g., a chamber 38, of the device 1. In someembodiments, the reference I-Vg curve and/or a chemical reaction I-Vgcurve may be generated in response to the biological material and/orchemical reaction that is to be detected and/or occurs over or near thechemically-sensitive field effect transistor, such as within a chamberor well 38 of the FET structure. In various embodiments, the processor150 may be configured to determine differences in relationships betweena generated reference I-Vg curve and/or chemical reaction I-Vg curve. Incertain instances, a circuitry component 140 may be included where thecircuitry component may include at least one analog-to-digital converter141 that is configured for converting analog signals, such as obtainedas a result of the performance of the reaction(s) within the reactionwell 38, or array of wells, into digital signals, such as may be sentback to the computing component 150 for further processing.

Accordingly, in another aspect of the disclosure, a chemically-sensitivefield effect transistor device 1 may be provided, wherein the device mayinclude a structure having a conductive source 22 and drain 24 as wellas having a surface or channel 26 extending from the conductive sourceto the conductive drain, such as where the surface or channel mayinclude a one-, two-, or three-dimensional transistor material 30. Thedevice 1 may also include a computing component 150 having or otherwisebeing associated with a processor such as where the processor isconfigured for generating a reference I-Vg curve and/or generating achemical reaction I-Vg curve, in response to the chemical reactionoccurring within a chamber 37 of the chemically-sensitive field effecttransistor 1, and may be configured to determine a difference betweenthe reference I-Vg curve and the chemical reaction I-Vg curve.Specifically, FIG. 6A depicts a graph illustrating an I-Vg curve callingout the various characteristics that may be used to categorize I-V gcurves, and FIG. 6B depicts a graph of an I-Vg curve illustrating theresults of a single difference and that of multiple differences.

Particularly, as can be seen with respect to FIG. 6B, the differencebetween the reference I-Vg curve measurement and the chemical reactionI-Vg curve measurement is a shift in a minimum point of the Vg value ofthe chemical reaction I-Vg curve relative to a minimum point of the Vgvalue of the reference I-Vg curve. As can be seen, this shift is fromleft to right along the Vg axis. Hence, as can be seen with respect toFIG. 6C, in some instances, a change in reaction conditions that resultin a change in the I-Vg curve may be demarcated by a shift in the I-Vgcurve, or as depicted in FIG. 6D, it may be demarcated by a change inthe shape of the I-Vg curve. More particularly, as exemplified in FIG.6C, in one embodiment, the difference between the reference I-Vg curveand the chemical reaction I-Vg curve may be a change in the slope of thechemical reaction I-Vg curve relative to a change in the slope of thereference I-V g curve. Likewise, as exemplified in FIG. 6D, thedifference between the reference I-Vg curve and the chemical reactionI-Vg curve may be an overall change in the shape of the chemicalreaction I-Vg curve relative to an overall change in shape of thereference I-Vg curve.

In other instances, as can be seen with respect to FIGS. 6E and 6F, thedifference between the reference I-Vg curve and the chemical reactionI-Vg curve may be a shift in an ion value of the chemical reaction I-Vgcurve relative to a shift in an ion value of the reference I-Vg curve,for instance, where the ion values are taken from a p-type (FIG. 6E) orn-type (FIG. 6F) section of the I-Vg curve (see FIG. 6A). For example,the measurements of the slopes may be taken from the steepest and/orflattest sections on the p-type and/or n-type portions of the I-Vgcurves. Specifically, FIGS. 6E and 6F depict graphs of I-Vg curvesillustrating a change in the level of the I-Vg curve where the ion is ina p-type region (FIG. 6E), and a change in the level of the I-Vg curvewhere the ion is in a n-type region (FIG. 6F).

Additionally, in particular instances, the difference between thereference I-Vg curve and the chemical reaction I-Vg curve may be a shiftin an Ioff value of the chemical reaction I-Vg curve relative to an Ioffvalue of the reference I-Vg curve. Particularly, FIG. 6G depicts a graphof an I-Vg curve illustrating a change in the level of the I-Vg curve(Ioff). More particularly, in such embodiments, as depicted in FIG. 6H,the difference in the overall shape of the I-Vg curves may be determinedby first fitting a polynomial or other fitting line to each of the I-Vgcurves and then comparing the coefficients of those fitting lines.Specifically, FIG. 6H depicts a graph of an I-Vg curve illustrating afit polynomial or other fitting line to curve and use coefficients asread criterion. In other embodiments, the difference between a referenceI-Vg curve and the chemical reaction I-Vg curve is based on more thanone chemical reaction I-V g curve. Further, FIG. 6I depicts a graph ofan I-Vg curve illustrating a check-slope of the I-Vg curve on one orboth sides (Gm & proportional to mobility), and use of a solution gateand backgate in combination to improve a signal and move the curve wheredesired.

It is to be noted, with respect to FIGS. 5B and 5C, when no microbead 60is present in the well structure 38, an electric signal may betransmitted to the computing component 150. In such an instance, theprocessor may be configured to eliminate from the measurement the numberof wells 38 that are unoccupied, or at least to compensate in themeasurement for the number of wells 38 that are unoccupied, such aswhere the measurement may be a shift in the I-V curve and/or I-Vg curve.Likewise, when two or more microbeads 60 a and 60 b are present in thewell structure 38, an electric signal may be transmitted to thecomputing component 150. In such an instance, the processor may beconfigured to eliminate from the measurement the number of wells 38containing multiple microbeads 60, or at least compensate in themeasurement for the number of wells 38 containing multiple microbeads60, such as where the measurement may be recognized as a shift in theI-V curve and/or I-Vg curve.

Accordingly, as can be seen with respect to FIGS. 6A-6I, in particularembodiments, the FET and/or processor may be configured to respond to ashift in the I-V or I-Vg curve, such as where the curve is shifted inresponse to the detection of a biological compound and/or the result ofa reaction taking place in or on a surface 26 of the FET device 1. Insome instances, the I-V/I-Vg curve may be produced and/or shifted inresponse to a chemical reaction occurring on a reaction layer 34/36and/or the surface of a 1D or 2D, e.g., graphene, surface 30 of thefield effect transistor 1, such as resulting from the detection of abiological compound or reaction occurring within the well structure 38of the device. Hence, the FET and/or processor may be configured so asto shift the I-V curve or I-Vg curve such as in response to the chemicalreaction.

For instance, FIG. 7A depicts a graph of an I-Vg curve for various pHvalues. Particularly, FIG. 7A illustrates the transfer characteristicsof a 20×40 micron graphene-on-SiO2 SGFET (“solution gated FET”) at aconstant drain-source voltage of Vds=50 mV for different pH values. FIG.7B depicts a graph of current increase vs. pH increase. Likewise, FIG.7C depicts a graph of frequency vs. normalized power spectral densityfor a silicon ISFET device. FIG. 7D illustrates a graph of frequency vs.normalized power spectral density for a typical graphene FET device ofthe disclosure. Additionally, FIG. 7E depicts a graph of frequency vs.normalized power spectral density for a graphene FET of the disclosure.FIG. 7F depicts a graph of noise vs. bias voltage, and FIG. 7G depicts agraph of Dirac voltage vs. current increase.

Hence, in various aspects of the disclosure, one or more elements and/ormethods, as herein described, may be used to shift a reference I-V orI-Vg curve and/or a chemical reaction I-Vg curve so that the differencebetween the reference I-Vg curve and a chemical reaction I-Vg curve ismore pronounced. However, in various embodiments, to make such adifference more pronounced, and thus, better able to be detected, thedevice may include a further structure 40, such as a membrane or otherelement that is configured for enhancing the ability of the processor todetermine the difference between various I-V and/or I-Vg curves. (See,for instance, FIG. 8A). Particularly, in various embodiments, a furtherstructured layer 4, e.g., a tertiary or quatemary structure, may also beprovided, such as where the further structured layer may be includedand/or present within the well or chamber, such as to enhance theability of the processor to determine the difference between the currentand/or voltages as well as their respective associated curves. Hence, inone aspect, a chemically-sensitive FET transistor 1 is provided wherethe FET is fabricated on a primary structure having a stackedconfiguration including an inorganic base layer 10, e.g., a siliconlayer; a dielectric structure and/or an organic or inorganic insulatorlayer 20, such as a silicon dioxide layer; a 1D, 2D, or 3D materiallayer 30, such as a carbon nanotube, nanowire, or graphene layer; anoxidation and/or passivation layer 34/36; and further having aconductive source 22 and drain 24 embedded in one or more of the layers,such as between and/or forming a gate structure 26, e.g., a solutiongate region 37.

Accordingly, as can be seen with respect to FIG. 8A, in variousembodiments, the gate region 26 may be configured so as to form achamber 37 and/or well 38 and the 1D or 2D material 30 and/or oxidationlayers 34 may be positioned between the conductive source 22 and drain24 in such a manner as to form a bottom surface of the chamber 37. Invarious instances, the structures may further include or otherwise beassociated with an integrated circuit and/or a processor, such as forgenerating and/or processing generated data, such as sensor deriveddata. And, further, in various embodiments, the chamber 37 may furtherinclude a membrane 40 or other element positioned above or between oneor more of the 1D, 2D, or 3D structure layer and/or the oxidation 34 andpassivation layers 36, such as where the membrane structure 40 isconfigured for enhancing the ability of the processor to determine thedifference between various I-V and/or I-Vg curves. For instance, FIG. 8Bdepicts a graph of an average sensitivity of a graphene FET (“gFET”)calculated as a function of liquid gate potential. The gFET of thepresent disclosure surpasses the theoretical 59 mVolt maximum for anISFET type device made of silicon. This difference is even morepronounced when a ion exclusive membrane 40 is included as part of thedevice.

In particular embodiments, therefore, as seen with respect to FIGS. 6and 8, a further structured layer 40, e.g., a secondary or tertiarystructure, may also be provided, such as where the further structuredlayer may be included and/or present within the well or chamber, such asto enhance the ability of the processor to determine the differencebetween the current and/or voltages as well as their respectiveassociated curves. More particularly, the additional structure mayinclude an ion-selective permeable membrane 40, such as an ion-selectivepermeable membrane that allows ions of interest to pass through themembrane 40 while blocking other indeterminate ions, such as to enhancethe ability of the processor to determine the difference between thereference I-V or I-Vg curve and the chemical reaction I-V or I-Vg curve,and thus enhance the ability of the processor to detect a desiredchemical reaction. In various instances, the FET 1 may be configuredsuch that the I-V or I-Vg curve(s) may be shifted so as to betterrespond to, detect, and/or otherwise determine a biological compoundand/or a chemical reaction, such as a biological compound and/or achemical reaction occurring on the 1D or 2D, e.g., graphene, surface 30of the chemically-sensitive field effect transistor 1. In particularinstances, the ion-selective permeable membrane 40 may include a 2Dtransistor material, e.g., graphene, which may or may not beelectrically connected to the source and/or drain layer and/or channel26.

Accordingly, in various instances, the chemically-sensitive field effecttransistor 1 may be fabricated on an integrated circuit wafer thatincludes a primary 10 and/or secondary 20 structure as well as a channelstructure 26, a processor and/or a tertiary structure 35, such as astructure forming one or more wells 38. For instance, the first and/orsecondary structures may include a conductive source 22 and a conductivedrain 24, which together with the other components of the FET 1 form achannel region 26. The channel 26 extends from the conductive source 22to the conductive drain 24, with the channel 26 formed between the two,where a one-dimensional or two-dimensional transistor material layer 30may be positioned above and/or may otherwise be in contact with thesource 22 and drain 24. As indicated above, the FET 1 may include aprocessor, such as where the processor is configured for generating oneor more of a reference I-Vg curve and a chemical reaction I-Vg curve,such as in response to a chemical reaction that is to be detected, forinstance, a reaction occurring over or near a reaction zone 26 of thechemically-sensitive field effect transistor 1. In particularembodiments, the processor is configured for determining a differencebetween the reference I-Vg curve and the chemical reaction I-Vg curve.Hence, in various embodiments, an additional structure 40 may beincluded, such as a structure that is configured for enhancing theability of the processor to determine this and other associateddifferences.

Particularly, in various embodiments, the additional structure may be anion-selective permeable membrane 40 that allows one or more ions ofinterest to pass through the membrane 40 while blocking other ions. Moreparticularly, the additional structure 40 may be configured so as toenhance the ability of the processor to determine the difference betweenthe reference I-Vg curve and the chemical reaction I-Vg curve, and thusfurther enhances the ability of the processor to detect a desiredchemical reaction. Accordingly, in various instances, the ion-selectivepermeable membrane 40 may be positioned within the well 38 and/or over apassivation layer 36, an ion sensitive or reaction layer 34, a 1D and/ora 2D or a 3D transistor material layer 30, and/or a dielectric layer 35that itself may be positioned over and/or otherwise form a part of thechamber 37 or channel 26. In certain embodiments, the membrane layer 40may be or otherwise be associated with an ion getter material, such asan ion getter material that traps ions that may or may not be relevantto the biological species and/or chemical reaction to be sensed and/ordetermined, such as to enhance the ability of the processor to determinethe difference between the reference I-V or I-Vg curve and/or thechemical reaction I-V or I-Vg curve. This may be useful because reducingthe number and/or amount of interfering ions, enhances the ability ofthe processor to detect the desired biological species and/or results ofthe chemical reactions. Particularly, the ion getter material may bearranged within proximity to the chamber 37 and/or surface 21 thereof sothat the action of gettering the unwanted ions improves the detectioncapability of the chemically-sensitive field effect transistor 1. Insome instances, one or more of the various layers herein, such as theion getter material may be placed over or between one or more of theother layers, such as the dielectric layer 20/35, oxide layer 34, or 2Dor 1D layers 30, positioned in proximity to one or more of the chambers,channels, or surfaces of the FET device 1.

In particular instances, the ion-selective permeable structure 40 mayinclude a polymer such as perfluorosulphonic material, aperfluorocarboxylic material, PEEK, PBI, Nafion or PTFE. In otherinstances, the ion-selective permeable structure may be composed of aninorganic material such as an oxide or a glass. In particular instances,the ion-selective permeable structure 40 may be applied to a surface,e.g., 21, of the FET such as by being deposited thereon, such as by aspincoating, anodization, PVD, or other sol gel methods. An additionalmaterial, e.g., HMDS, may also be included so as to manage theinteraction of the chamber 37 and/or channel 26 and/or associated oxidelayer 20/35 and/or an underlying 2D or 1D transistor layer 30. Forinstance, a chemically-sensitive field effect transistor 1 of thedisclosure may include an additional structure that includes a 2Dtransistor channel or surface which may include an ion-sensitivematerial over the channel or surface. In such an instance, the materialmay be sensitive to ions that are different from the ions associatedwith the biological molecule or chemical reaction that is to bedetected. Particularly, the ion-selective permeable structure 40 mayadditionally be composed of an ion sensitive 1D or 2D transistormaterial, such as graphene, that is in addition to the 1D or 2D materiallayer 30, and is not electrically connected to the channel 26.

In certain instances, the ion-selective permeable structure 40 may bepositioned over the ion sensitive layer 30 that itself may be positionedover the channel structure or surface 26. As indicated, the additionalstructure 40 may be composed of an ion getter material, wherein the iongetter material is configured to trap ions that are not relevant to thechemical reaction to be determined. Accordingly, in some instances, asuitably configured membrane 40 and/or additional structure, e.g., HMDSor other siloxane, may be useful because the action of sensing ions thatare different from the ions associated with the biologics and/orchemical reactions that are to be detected allows the processor tofilter out the signal from the unwanted ions from the signal of the ionsof interest. In particular instances, the HMDS material may bepositioned under the graphene. Accordingly, in various instances, anexemplary ion-selective permeable membrane 40 and/or an additionalgetter structure may be positioned over a channel structure 26, wherethese structures are configured so as to only allow ions of interest totravel through them. In particular instances, the getter material may bepositioned within the chamber 37 or elsewhere on the chip or in thepackage so as to attract unwanted ions. Another alternative would be toinclude another ion-selective functional layer(s) over some of thesensors which can detect the presence of contaminants or unwanted ionsso that their interaction with the sensor and thus the determination ofthe sensor reaction to the desired ion can be filtered out.

In all of these instances, the action of trapping ions that are notrelevant to the chemical reaction to be determined enhances the abilityof the processor to determine the difference between the reference I-V gcurve and the chemical reaction I-Vg curve, e.g., because there arefewer interfering ions. In such instances, the membrane 40 and/or iongetter material may be arranged within proximity to a reaction zone 26that is in proximity to a channel region so that the action of getteringthe unwanted ions improves the detection capability of thechemically-sensitive field effect transistor. Alternatively, the iongetter material may be placed over a dielectric layer that is inproximity to one or more of the reaction zones 26 and/or channels.

In another aspect, the present gFET integrated circuits, sensors, and/orarrays of the disclosure may be fabricated such as using any suitablecomplementary metal-oxide semiconductor (CMOS) processing techniquesknown in the art. In certain instances, such a CMOS processing techniquemay be configured to increase the measurement sensitivity and/oraccuracy of the sensor and/or array, and at the same time facilitatesignificantly small sensor sizes and dense gFET chamber sensor regions.Particularly, the improved fabrication techniques herein describedemploying a 1D, 2D, 3D, and/or oxide as a reaction layer provide forrapid data acquisition from small sensors to large and dense arrays ofsensors. In particular embodiments, where an ion-selective permeablemembrane is included, the membrane layer may include a polymer, such asa perfluorosulphonic material, a perfluorocarboxylic material, PEEK,PBI, Nafion, and/or PTFE. In some embodiments, the ion-selectivepermeable membrane may include an inorganic material, such as an oxideor a glass. One or more of the various layers, e.g., the reaction,passivation, and/or permeable membrane layers may be fabricated orotherwise applied by a spin-coating, anodization, PVD, and/or sol gelmethod.

Accordingly, when using the device for sequencing a nucleic acid sample,the target nucleic acid sample may be coupled to or in proximity withthe graphene coated surface of the reaction zone. This template sequencemay then be sequenced and/or analyzed by performing one or more of thefollowing steps. For example, a primer, and/or a polymerase, e.g., anRNA and/or DNA polymerase, and/or one or more substrates, e.g.deoxynucleotide triphosphates dATP, dGTP, dCTP, and dTTP, may be added,e.g., sequentially, to the reaction chamber, such as after thehybridization reaction begins so as to induce an elongation reaction.Once the appropriate substrate hybridizes to its complement in thetemplate sequence, there will be a concomitant change in the individualelectrical characteristic voltage, e.g., the source-drain voltage (Vsd),measured as a result of the new local gating effect.

Hence, for every elongation reaction with the appropriate, e.g.,complementary, substrate there will be a change in the characteristicvoltage. For instance, as described herein, a field-effect device fornucleic acid sequencing and/or gene detection is disposed in a samplechamber of a flow cell, and a sample solution, e.g., containing apolymerase and one or more substrates, may be introduced to the samplesolution chamber. In various embodiments, a reference electrode may bedisposed upstream, downstream or in fluid contact with the field effectdevice and/or the source and/or drain may themselves serve aselectrodes, such as for hybridization detection, and gate voltage may beapplied whenever needed.

Particularly, in an exemplary elongation reaction, polynucleotides aresynthesized if the added substrate is complementary to the base sequenceof the target DNA primer and/or template. If the added substrate is notcomplementary to the next available base sequence, hybridization doesnot occur and there is no elongation. Since nucleic acids, such as DNAsand RNAs, have a negative charge in aqueous solutions, hybridizationresulting in elongation can be incrementally determined by the change inthe charge density in the reaction chamber 30. And because thesubstrates are added sequentially, it can readily be determined whichnucleotide bound to the template thereby facilitating the elongationreaction. Accordingly, as a result of elongation, the negative charge onthe graphene gate surface, insulating film surface, and/or the sidewallsurface of the reaction chamber will be increased. This increase maythen be detected, such as a change in the gate source voltage, asdescribed in detail herein. By determining the addition of whichsubstrate resulted in a signal of change in gate-source voltage, thebase sequence identity of the target nucleic acid can be determinedand/or analyzed.

More specifically, the field-effect transistor, such as for nucleic acidelongation and/or hybridization detection, may be associated with abuffered solution that is added to the reaction chamber, which can thenbe used to determine if an elongation reaction has taken place.Particularly, once the template is associated with the substrate, thereaction mixture containing a polymerase, e.g., a Taq polymerase, and afirst nucleic acid substrate, e.g., a dATP, is added to the buffersolution to carry out the elongation reaction on the graphene gatecoated insulating film of the reaction chamber surface. If the dATP is acomplement to the next available reaction site in the isolated templatea binding event, e.g., a hybridization reaction, will occur and theantisense strand of the growing sequence will be elongated, and detectedby the GFET transistor.

For example, if adenine (A) is complementary to the base thymine (T) onthe target template adjacent to the 3′-terminus of the nucleic acidtemplate, an elongation reaction occurs, resulting in synthesis of oneadenine. In such instance, the enzyme, Taq DNA polymerase, and thesubstrate may be washed away from the gate portion and reaction chamber,and a buffer solution, e.g., a phosphoric acid buffer solution, e.g.,having a pH of about 6, may be introduced on the graphene gate surfaceto measure changes in the source-drain voltage. If hybridization hasoccurred there will be a change in the source-drain voltage and it willbe detected. However, if the dATP is not a match, there will be nohybridization, and if no hybridization, there will be no elongation.Consequently, a second reaction mixture containing another, differentnucleotide substrate, e.g., dCTP and the enzyme polymerase, and the likewill be added to the reaction chamber under conditions suitable forhybridization, which if it occurs will be detected by the GFET. If not,then the steps will be repeated with the next substrate. These steps maybe repeated until the nucleic acid sample has been completely sequenced.In various instances, the temperature within the reaction chamber may becontrolled, for instance, it may be set to 74° C., such as by using atemperature sensor and/or a heater integrated in the field-effectdevice.

Consequently, if a hybridization reaction takes place there will be aresultant change to the threshold voltage, which will be increased,e.g., by 4 mV, from before the elongation reaction. The shift of thethreshold voltage in the positive direction indicates that a negativecharge was generated on the graphene gate surface. It can be understoodfrom this that synthesis of one base caused by the elongation reactionwas detectable as a change in threshold voltage. A second elongationreaction may then take place and be repeated until the entire targetnucleic acid has been sequenced.

Accordingly, FIG. 9A is an illustration of electrowetting forbiomolecule attachment, as disclosed herein. FIG. 9B is an illustrationof electrophoresis for biomolecule attachment. FIG. 9C is anillustration of microfluidics for biomolecule attachment. And FIG. 30 isan illustration of an optical readout of DNA sequencing usingnanomaterials.

More particularly, in such a configuration as represented in thefigures, the drain current of the transistor may be modulated by theelectrical charge carried by the nucleotide molecules involved in thehybridization and/or sequencing reactions. For example, after a bindingevent, the charge in the reaction zone increases resulting in a changein the output current that may be measured. Such a measurement may bemade in accordance with the following equation:

More particularly, in such a configuration as represented in thefigures, the drain 26 current of the transistor 20 may be modulated bythe electrical charge carried by the nucleotide molecules involved inthe hybridization and/or sequencing reactions. For example, after abinding event, the charge in the reaction zone increases resulting in achange in the output current that may be measured. Such a measurementmay be made in accordance with the following equation:

$V_{THF} = {V_{{TH}\; 0} - \frac{Q_{com} + Q_{0}}{C_{C} + C_{F}}}$

Such as where C_(C) represents the current at the control capacitor, andC_(F) represents the current at the parasitic capacitor. V_(THF)represents the effective threshold voltage of the transistor 20, andV_(TH0) represents the native threshold voltage. Q₀ represents theelectric charge initially trapped in the floating gate, and Q_(DNA)represents the total charge of hybridization complex.

For instance, a nucleic acid from a sample to be sequenced orrepresentative of a probe to be targeted may be immobilized on thebottom surface or the sidewall of the sample solution well chamber. ATaq DNA polymerase and a nucleotide substrate may then be introduced tothe sample solution chamber to induce an elongation reaction. As aresult, DNAs may be synthesized along the surface in the vertical orlateral direction, e.g., in parallel to the surface of the graphenecoated gate surfaces. In such an instance, as the source-drain currentvs gate voltage characteristic changes by the electrostatic interactionwith the charged particles (electrons) in the well, and the synthesis ofthe DNA is in the direction that is transverse or parallel to thegraphene gate surface, this keeps the distance between the DNA and theelectrons constant, thereby helping to maintain a constant electrostaticinteraction. Thus, the base sequence of a template nucleic acid having alarge base length can be sequenced and/or analyzed. In otherembodiments, a nucleic acid probe may be immobilized on the surface ofthe reaction zone, as described above, and used in a hybridizationreaction so as to detect genetic variation and/or the presence of agenetic disease.

In various instances, in order to conduct parallel analysis of aplurality of nucleic acid templates, the number of the transistors maybe equal to or higher than the number and/or types of DNAs to besequenced and/or analyzed. In certain instances, each nucleic acidtemplate or probe may be an oligonucleotide or a fragment of DNA or RNAthat may be constituted from about 100 to about 1000 bases, such as from200 to about 800 bases, for instance, from about 300 or about 500 basesto about 600 or 700 bases or more or somewhere in between. However, invarious instances, a fragment of nucleic acid having 100 bases or fewermay also be used.

Additionally, as indicated above, the present device may also be used invarious different DNA/RNA hybridization reactions, such as for thepurpose of determining a genetic variation and/or for detecting thepresence of a genetic marker for a disease. In such an instance, anucleic acid probe may be coupled to a bottom or side graphene coatedsurface of the reaction chamber, per above. As indicated, the probe maybe of any suitable length but in various instances from about 5 or 10 toabout 1000 bases, such as from 20 or about 50 to about 700 or about 800bases, for instance, from about 100 or about 200 bases to about 300bases including about 400 or about 500 bases to about 600 or 700 basesor more or somewhere in between.

For instance, in one exemplary instance, a nucleic acid probe containingabout 10 to 15 bases coding for a gene sequence of interest that hasbeen previously amplified, such as by polymerase chain reaction (PCR),may be immobilized on the gate, gate insulating film or side surface ofthe reaction chamber of the field-effect transistor. For example, onceisolated and amplified, the base of the template may be modified so asto be attached to the graphene coated surface, and/or may be coupled toa secondary substrate, such as a glass or plastic bead that has beenchemically treated so as to be coupled therewith. Once immobilized, thereaction chamber containing the probes, either on a secondary substrateor directly coupled with a chamber surface, may be reacted with a samplesolution containing a number genes including a target gene of interestto be measured such that when a nucleic acid probe having acomplementary base sequence to the target gene is immobilized on thegate, gate insulating film or the sidewall surface of the samplesolution well structure, or on a secondary substrate immobilized withinthe reaction chamber of the field-effect device for gene detection, thetarget gene hybridizes with the nucleic acid probe under appropriatereaction conditions and the target gene and the nucleic acid probe forma double strand, the result of which hybridization reaction may bedetected.

As depicted in FIG. 10A, a gFET array sets forth a two dimensional gFETsensor array chip that in this instance is based on a column and rowdesign, although other designs are also possible. As can be seen withrespect to FIG. 10B, the system further includes a row and columndecoder, as well as circuitry for performing the requisite sensing,detecting, and processing so as to measure the sensory data. Hence, alsoincluded is sensing, measurement, and other associated readout data.

Accordingly, as can be seen with respect to FIGS. 10A and 10B, invarious instances, a one or two-dimensional GFET array, as describedherein, may be fabricated on a microchip in accordance with the methodsherein disclosed. In various instances, the array chip may include anumber of GFET sensors that may be arranged in columns and/or rows. Atypical number of sensors may include GFET sensor elements, describedherein as “sensors,” that may be arranged in a 16 sensor by 16 sensorcolumn/row array configuration. As depicted, the array includes twocolumns, but typically may include sixteen columns, arranged side byside, where each column includes 16 rows. Particularly, each column ofthe array includes up to 16 sensors. Each column may be configured so asto include a current source I_(SOURCE) that may be shared by all sensorsof the column. However, in various other embodiments, each sensor mayhave its own current source, or the array itself may have a singlecurrent source. Additionally, each GFET sensor may include a GFET, asdescribed above, having an electrically coupled source and/or drainand/or body, and may further include one or more switches, such as aplurality of switches S1 and S2 that may be configured so as to beresponsive to one of the up to sixteen row select signals (RSEL, andit's complements). More particularly, a row select signal and itscomplement may be generated simultaneously to “enable” or select a givensensor of the selected column, and such signal pairs may be generated insome sequence to successively enable different sensors of the column,e.g., together or one at a time, such as sequentially.

A row decoder may also be provided as part of the system. In such aninstance, the row decoder may be configured so as to provide up tosixteen pairs of complementary row select signals, wherein each pair ofrow select signals may be adapted so as to simultaneously orsequentially enable one sensor in each column so as to provide a set ofcolumn output signals from the array, e.g., based on the respectivesource voltages VSa through VSb, etc. of the enabled row of GFETs. Therow decoder may be implemented as a conventional four-to-sixteen decoder(e.g., a four-bit binary input ROW1-ROW4 to select one of 24 outputs).The set of column output signals VSa through VSb for an enabled row ofthe array is applied to switching logic, which may be configured toinclude up to sixteen transmission gates Sa through Sb (e.g., onetransmission gate for each output signal).

As above, each transmission gate of the switching logic may beimplemented using an n-channel or p-channel MOSFET, in a bottom or topgate configuration, or both to ensure a sufficient dynamic range foreach of the output signals V_(Sa) through V_(Sb). The column decoder,like the row decoder, may be implemented as a conventionalfour-to-sixteen decoder and may be controlled via the four-bit binaryinput COL₁-COL₄ to enable one of the transmission gates Sa through Sb ofthe switching logic at any given time, so as to provide a single outputsignal V_(S) from the switching logic. This output signal V_(S) may beapplied to a 10-bit analog to digital converter (ADC) to provide adigital representation D₁-D₁₀ of the output signal V_(S) correspondingto a given sensor of the array.

As noted earlier, individual GFETs and arrays of GFETs such as thosediscussed above may be employed as sensing devices in a variety ofapplications involving chemistry and biology. In particular, such GFETsmay be employed as pH sensors in various processes involving nucleicacids such as DNA. In general, the development of rapid and sensitivenucleic acid hybridization and sequencing methods, as herein described,e.g., utilizing automated DNA sequencers, may significantly advance theunderstanding of biology.

It should be noted, that with respect to the various arrays disclosedherein according to various embodiments of the present disclosure may befabricated according to conventional CMOS fabrication techniques, asdescribed above, as well as modified CMOS fabrication techniques (e.g.,to facilitate realization of various functional aspects of the GFETarrays discussed herein, such as additional deposition of grapheneand/or other passivation materials, process steps to mitigate trappedcharge, etc.) and other semiconductor fabrication techniques beyondthose conventionally employed in typical CMOS fabrication (e.g.,BiCMOS). Additionally, various lithography techniques may be employed aspart of an array fabrication process. For example, in one exemplaryimplementation, a lithography technique may be employed in whichappropriately designed blocks are “stitched” together by overlapping theedges of a step and repeat lithography exposures on a wafer substrate byapproximately 0.2 micrometers. In a single exposure, the maximum diesize typically is approximately 21 millimeters by 21 millimeters. Byselectively exposing different blocks (sides, top & bottoms, core, etc.)very large chips can be defined on a wafer (up to a maximum, in theextreme, of one chip per wafer, commonly referred to as “wafer scaleintegration”).

In one embodiment, as can be seen with respect to FIG. 2E, the arrayincludes 512 columns with corresponding column bias/readout circuitry(one for each column), wherein each column includes geometrically squaresensors, each having a size of approximately 9 micrometers by 9micrometers (e.g., the array may be up to 512 columns by 512 rows). Invarious instances, the entire array (including sensors together withassociated row and column select circuitry and column bias/readoutcircuitry) may be fabricated on a semiconductor die as an applicationspecific integrated circuit (ASIC), structured ASIC, or as a field gatedarray, such as having dimensions of approximately 7 millimeters by 7millimeters.

Various power supply and bias voltages useful for array operation areprovided to the array via electrical connections (e.g., pins, metalpads) and labeled for simplicity in block as “supply and biasconnections.” The array may also include a row select shift register,one or more, e.g., two sets of column select shift registers, and one ormore, e.g., two, output drivers, which output drivers are configured toprovide two parallel output signals from the array, V_(outa) andV_(outb), representing sensor measurements. The various power supply andbias voltages, control signals for the row and column shift registers,and control signals for the column bias/readout circuitry may beprovided by an array controller, which controller may also read theoutput signals V_(outa) and V_(outb) (and other optionalstatus/diagnostic signals) from the array. Configuring the array suchthat multiple regions (e.g., multiple columns) of the array may be readat the same time via multiple parallel array outputs (e.g., V_(outa) andV_(outb)) facilitates increased data acquisition rates.

Accordingly, in various instances, an integrated circuit for performinga sequencing reaction is provided, such as where the sequencing reactioninvolves the sequencing of strands of nucleic acids, as describedherein. In various instances, the integrated circuit may include asubstrate and an array of graphene field effect transistors arranged onthe substrate. In such an instance, one or more of, e.g., each, of thegraphene field effect transistors may include a primary layer forming abase layer, and a secondary, e.g., intermediary, layer positioned overor otherwise associated with the primary layer, the secondary layerbeing formed of a first nonconductive material and including a sourceand a drain formed in the first nonconductive material, the source anddrain being separated one from the other by a channel, and being formedof an electrically conductive material. In certain instances, a tertiarylayer may be positioned over the secondary layer, such as where thetertiary layer includes a gate formed over the channel to electricallyconnect the source and the drain. In such an instance, the gate may beformed of a graphene layer. The tertiary layer may additionally includea surface structure that overlaps the source and the drain in thesecondary layer, the surface structure further defining a well havingside walls and a bottom that extends over at least a portion of thegraphene layer of the gate so as to form a reaction chamber for theperformance of the sequencing reaction. In particular embodiments, achemically-sensitive bead provided in one or more wells of the array ofgraphene field effect transistors, such as where one or more, e.g.,each, chemically-sensitive bead may be configured with one or morereactants to interact with portions of the strands of nucleic acids suchthat the associated graphene field effect transistor detects a change inion concentration of the reactants by a change in current flow from thesource to the drain via an activation of the graphene layer.

It should be noted that, in various embodiments of the array, one ormore of the columns, e.g., the first and last columns, as well as thefirst and/or last sensors of each of the columns may be configured as“reference” or “dummy” sensors. For instance, the dummy sensors of anarray, e.g., the topmost metal layer of each dummy sensor may be tied tothe same metal layer of other dummy sensors and may be made accessibleas a terminal of the chip, which in turn may be coupled to a referencevoltage VREF. Such reference voltage VREF may be applied to thebias/readout circuitry of respective columns of the array. In someexemplary implementations, preliminary test/evaluation data may beacquired from the array based on applying the reference voltage VREF andselecting and reading out dummy sensors, and/or reading out columnsbased on the direct application of VREF to respective column buffers(e.g., via the CAL signal), to facilitate offset determination (e.g.,sensor-to-sensor and column-to-column variances) and array calibration.

The calibration data can be stored for each sensor location either justprior to a sequencing session, or preferentially at the end of thedevice manufacturing process. The calibration data can be stored on-chipin non-volatile memory.

Additionally, in a further aspect of the present disclosure, a fieldeffect transistor having a chamber and/or channel including a 1D or 2Dand/or 3D material may be provided, such as where the 1D or 2D and/or 3Dmaterial is present within and/or proximate the chamber and/or channeland configured in such a manner so that the chamber and/or channelgeometry may be optimized so as to maximize the ratio of channel width(W) to channel length (L). In various instances, this can be donethrough the use of interdigitated source and drain electrode geometries,such as in a single plane or, in other embodiments, such optimizationmay be achieved through the use of one or more 3D electrode structures,such as configured to at least partially or fully circumscribe thechamber or well. For instance, as can be seen with respect to FIG. 11,various source 22 and/or drain 24 electrodes may be configured asthree-dimensional (3D) structures that are adapted so as to interactwith one another in such a manner to more accurately detect the presenceof a chemical reaction, e.g., the presence of a biomolecule, that occursproximate the source and drain electrodes.

In various instances, the source 22 and drain electrodes 24, as setforth in FIG. 11 may be formed in such a manner so as to have aninterdigitated configuration, such as where one or more of theelectrodes, or a portion thereof, are adapted so as to be fit one withinthe other, such as where one electrode portion is configured as animpingement member, and the other is configured as a receiving member.In particular embodiments, the source 22 and drain 24 electrodes areconfigured so as to include pronged, fork-like appendages that arecapable of being fitted one within the cavity of the other, such asbetween adjacent prong members. For example, as seen with respect toFIG. 11, the source and drain electrodes may form electrode pairs, suchas where one or more of the source 22 and drain 24 electrodes may have aplanar and/or extended and/or interdigitated design, such as where one,e.g., the first, of the electrode pair forms one or more cavities andthe other, e.g., the second, of the electrode pair forms an impingementmember for insertion within the one or more of the cavities of the firstelectrode. Particularly, in various implementations, one or more of theelectrode pairs may have a linear configuration, while the second of thepair may have a linear, curved, or curvilinear configuration. Inparticular embodiments, both the source 22 and drain 24 electrodes mayboth be curvilinear or curved.

More particularly, as can be seen with respect to FIG. 12, a FET sensor1 having a well structure 38 is provided. Particularly, FIG. 12 depictsa cross-section of a well opening stopping on an analyte-sensitivelayer. For instance, FIG. 12 provides a substrate, such as siliconand/or silicon dioxide substrate 10/20, where the substrate isconfigured so as to include a chamber, such as a chamber having a formedwell 38 that may be positioned over an analyte-sensitive layer 35 thatmay be positioned on top of that substrate 10 and/or an associated oxidelayer 20. For instance, in accordance with the methods disclosed herein,such a well 38 may be formed by any suitable method such as by a dryetching process, such as by a plasma or RIE process. In particularinstances, the etching process may be selective to the well material sothat the well etch can be stopped on the analyte-sensitive layer withoutsignificant damage or etching of the analyte-sensitive layer.

Additionally, as shown in FIG. 13 one or more additionalanalyte-sensitive layers 34 can be included in the FET, such as formedon the sidewalls 39 and bottom 21 of the well 38. For instance, FIG. 13depicts a cut-away view of a substrate 10, wherein the substrateincludes a well having a chamber therein, such as a chamber defined byone or more walls. In various instances, one or more of the walls mayhave an analyte-sensitive layer coating the walls of the well.Particularly, a substrate 10 may be provided such as where the substrate10 may be formed of a silicon layer and may include one or moreadditional layers, such as one or more dielectric layers 20 and/or 35,which dielectric layers may be composed of silicon dioxide. Imbeddedwithin one or more of these layers my be a pair of electrodes, such as asource electrode 22 and a drain electrode 24, which may be in one ofmore of the configurations set forth in FIG. 11, or other suitableconfiguration. As can be seen, one or more of the dielectric layers 20and/or 35 may be configured so as to include a well structure 38, whichstructure may further be adapted so as to include one or more additionallayers 34, such as a plurality of analyte-sensitive layers 34 a and 34b. For instance, one of the analyte sensitive layers 34 a may bepositioned on a bottom surface 21 of the well 38, such as layered upon achannel member 26, such as upon a graphene structure layer 30 positionedwithin the channel 26. Additionally, another analyte sensitive layer 34b may be layered upon one or more of the well bounding members 39 a and39 b.

Further, with respect to FIG. 14, as previously noted, in variousinstances, it may be desirable to increase the ratio of the channelwidth W to the channel length L (e.g., W/L). For instance, FIG. 14depicts a FET device, as herein described, wherein the FET includes awell having one or more walls that may be configured to produce orotherwise include a 3D interdigitated electrodes. Particularly, having awell structure, as set forth in FIGS. 12 and 13, allows the formation ofsource 22 and drain 24 electrodes not only on the bottom of the well 21,but also may be fabricated on the sides of the well 39, such as in oneor more of the configurations set forth in FIG. 11. Specifically, FIG.14 depicts a well structure in a cross-section view that has one or moresurfaces that have been configured for allowing one or more electrodesto be fabricated therein. In this instance, the source electrodes 22 anddrain electrodes 24 are interdigitated and positioned both on the bottom21 of the well and on the sides 39 of the well. Many geometric patternscan be designed for source 22 and drain 24 electrodes to cover both thesides and bottom of the wells and the pattern shown in FIG. 14 is butone example, while FIG. 15 is another example, such as where the wellincludes a transistor material or an analyte-sensitive layer that may bepositioned or otherwise coated over the surface of the well boundingmember and/or one or more electrodes configured therein.

For example, one possibility for forming the source 22 and drain 24electrodes in the well 38, such as in a 3D structure as set forthherein, is to use a photopatterning or photolithographic process. Insuch an instance, a mask with the desired pattern(s) may be used totransfer a pattern onto a photosensitive photoresist material. Thepattern in the photoresist material can be used to likewise define apattern in the conductive electrodes (e.g., by etching, lift-off,plating, and/or other processes known in the art). For instance, it ispossible by employing the right optics to expose photoresist into deeptrenches and/or wells so as to be able to define conductive traces inthose deep trenches or wells. An example of this is shown in FIG. 16,which presents a depiction of an interdigitated well structure that hasbeen fabricated using lithographic methods. Other techniques that canaddress patterning of photoresist in deep trenches or wells are laser,electron beam, and/or plasma, and the like.

Particularly, in various instances, once the source 22 and drain 24electrodes are formed on the sides 39 of the well 38 the channel 26 maybe formed over the electrodes. The process used to form the transistorchannel 26 may be by any suitable process, but may depend on thematerials being deposited and the presence of process limits imposed byother devices incorporated into the sensor. For instance, asilicon-based CMOS wafer with conventional transistors (e.g., formedfrom doped regions in the silicon and polysilicon or metal gates) willtypically have a processing temperature limit of 350 to 400 degrees C.,above which damage to those transistors may occur. So for a CMOS waferwith added sensors, the deposition of the materials making up thosesensors will typically be lower than 400 degrees C., which can beaccomplished either by a low temperature in-situ deposition processes,and/or by creating the desired sensor materials separately andtransferring them to the appropriate locations on the CMOS wafer.

In some instances, a 1D or 2D transistor material 30 can be formedseparate from the CMOS wafer and then be transferred onto the electrodestructures in the wells 38, as shown in FIG. 15. In another instance,another option may be to deposit a transistor channel material on theelectrodes 22, 24 and well walls 21, 39. This may be accomplished by lowtemperature (below 400 degrees C.) deposition of amorphous silicon orsuitable 2D material by any suitable means including, but not limitedto: CVD, ALD, PVD (e.g., evaporation and/or sputtering), PECVD, and/orthe like. Likewise, as depicted in FIG. 15, one or more of these methodscan be used to coat the interior chamber of the well structure with atransistor material, such as an analyte-sensitive layer.

FIG. 17 depicts a top-plane view of a geometric pattern of source 22 anddrain 24 electrodes that might be found at the side 39 and bottom 21 ofthe well structure 38 shown in cross-section view in FIG. 18. Forinstance, FIG. 17 depicts the use of alternating vertical metal sourceand drain electrode layers, which may be positioned, such as within achamber or the bounding member(s) defining the chamber, so as to createan interdigitated type of effect and thereby maximize the of ratiochannel width to channel length, as herein described. Particularly,FIGS. 17 and 18 depict a sensor 1 composed of a substrate material,e.g., 10, 20, and/or 35, and having a chamber 38 formed therein, such asby etching. The chamber 38 includes a wall 39 and/or a bottom surface 21having a plurality of electrodes disposed therein, such as a sourceelectrode 22 and a drain electrode 24, such as where the electrodes havebeen configured in an interdigitated manner. It is to be noted thatalthough a particular electrode configuration has been depicted, anysuitable configuration can be implemented, such as those depicted inFIG. 11.

To demonstrate the desirability of forming 3 dimensional electrodestructures on the well surfaces 39 and/or 21, a comparison of the ratioof channel width to channel length (W/L) can be made of a device thatonly has electrodes 22, 24 on the well bottom 21 versus one withelectrodes on the well bottom 21 and well walls 39. For instance, withrespect to the well structure depicted in FIGS. 17 and 18, e.g., with anominal 1 micron well diameter (at the well bottom 21), the channellength of channels 26 either at the well bottom 21 or on the well walls39 is 100 nm, for example. For the well bottom 21, the channel 26 widthis given by the formula 2πR (it is the distance of the channel definedby the gap between the source 22 and drain 24 electrodes. If we assumethe radius of the channel 26 is 150 nm, then the channel width is about945 nm. This results in a W/L of about 9.45. Further, as depicted inFIGS. 17 and 18, there are multiple electrode layers, such as in avertically stacked configuration that circumscribes and/or surrounds thewell opening 37. In such an instance, the channel length may be about100 nm. In this instance the channel width is contributed by thecircular gap between each electrode layer times the number of such gaps.

For example, for 6 gaps, where the well diameter is 1000 nm, the channelwidth due to the sidewall structures is: W_(vertical)=2πrN=6.3×500nm×number of levels=3150 nm×6=18900 nm. Further, if the channel width atthe well bottom is added, a total channel width is 19845 nm and a W/L of198. This is more than a 20 times higher W/L than the case with anelectrode structure only on the well bottom. As described above, theelectrode structures 22, 24 on the well sidewalls 39 and at the wellbottom 21 may be covered by a transistor material, such as depicted inFIG. 19. Furthermore, an analyte-sensitive layer 34 may be depositedover the electrodes on the well boundary walls 39 and bottom 21.Particularly, FIG. 19 depicts a well chamber 38, wherein the chamber 18may be configured to include a transistor material or ananalyte-sensitive layer.

In various instances, the source 22 and drain 24 electrodes can formelectrode pairs that are separated one from the other by a distance suchas to from an interdigitated source 22 and drain 24 electrode pair. Aspresented in FIG. 20, the source 22 and drain 24 electrode pairs may beconfigured so as to form a channel between the two electrodes, such asin the space between the two electrodes. In such instances, as depictedin FIG. 20, the channel may be comprised of or otherwise contain a 1D or2D channel material, such as a carbon nanotube and/or graphene layer.Hence, an option for forming one or more channels 26 with small lengthsand high effective widths is to vertically alternate not only the source22 and drain 24 electrode layers, but also the transistor channelmaterial (e.g., 1D or 2D material) layers, as depicted in the wellstructure cross-section as shown FIG. 20. In this case, the channelmaterial 30, e.g., a series of graphene layers, is interspersed betweensource 22 and drain 24 electrode layers. Hence, performing the samecalculation as before, but in this case using a channel length of 0.345nm (the thickness of a single layer of graphene is 0.345 nm) results ina W/L ratio of 57,522 which is more than 290 times higher than theprevious calculation and demonstrates the effectiveness of using thinchannel material layers as part of the device structure.

FIG. 21 depicts one implementation of a process flow that may beemployed to form the source 22 and drain 24 electrode layers as well asthe 1D or 2D sensor material layer 30. For instance, FIG. 21A depictsthe bottom 21 of a substrate or well material that may be configured soas to include a conductive source 22 and drain 24 electrode. These may,for example, be fabricated and/or formed by various fabricationprocesses as herein described and/or known in the art, such as by usinga damascene metal process. The surface of the device may be ChemicallyMechanically Polished (CMP), such as after the conductive source 22 anddrain 24 electrodes are formed in the well bottom 21. It is to be noted,that FIG. 21A depicts the conductive source electrode 22 and conductivedrain electrode 24 in different layers, and at any given level or layerof the device, where electrodes are formed, the electrodes can be formedof the same material during the same process step or different. Forexample the source 22 and drain 24 electrodes of FIG. 21A could becomprised primarily of copper that is deposited by an electroplatingprocess with both types of electrodes formed in the same process step.

FIG. 21B depicts a layer of a 1D or 2D channel material 30 that has beendeposited over the electrodes in the well bottom 21. The channelmaterial 30 may be patterned so that it just covers all of theunderlying conductive electrode pattern or it may be sized smaller orlarger than the underlying electrode pattern—as long as it overlaps witha portion of the electrodes.

The next step, shown in FIG. 21C, is the deposition of an insulatinglayer 35 and then the formation of a trench in that layer.

FIG. 21D shows the trench being filled by conductive electrode material.During this step vertical electrode connections, e.g., vias, may beformed outside of the electrode patterns. Such vias may be stacked layerby layer as the process progresses allowing the vertical interconnectionof source electrodes 22 on different layers, and allowing the verticalinterconnection of drain electrodes 24 on different layers.

These process steps may be repeated in FIGS. 21E, 21F and 21G to createvertical layers of alternating source electrode 22, transistor channelmaterial 30, and drain electrode 24, such as in an interdigitatedconfiguration, as herein described. Duplicating these steps for furtherrepetitions allows higher numbers of alternating source electrode 22,transistor channel material 30, and drain electrode 24 layers to beformed. When the selected number of layers have been formed the centralportion of the well 38 can be etched (e.g., by plasma, RIE, DRIE or asimilar process) as shown in FIG. 21h . This results in the fully formedlayer stack depicted in FIG. 20.

FIGS. 22A and 22B depict a different embodiment for forming alternatinglayers of electrodes 22, 24 and transistor channel material 30. In thiscase vias, e.g., through-holes, trenches, and/or slots may be formed inthe transistor channel material 30 as shown in FIG. 22B. In a subsequentstep (not shown in the figures) the formation of the electrode materialover or on the patterned channel material will also fill these vias.This allows not only a surface area connection from the electrode to thechannel material but also an edge connection to the channel material(e.g., in the via the electrode material may contact the edge of thechannel material). In some materials, such as graphene, it is known thatedge connections from electrodes to the graphene channel material mayresult in lower contact resistance between the two materials and bettertransistor performance.

Additionally, FIG. 23 depicts an alternate well structure 1. In thisinstance grooves or trenches 61 may be formed in the wall boundaries ofthe well 39. These grooves 61 can help to align and capture the 1Dand/or 2D transistor channel material—such as carbon nanotubes orsilicon wires. Accordingly, FIG. 23 depicts a well that uses carbonnanotubes to create interdigitated transistors, such as in a verticaldirection.

Accordingly, in various aspects of the disclosure, achemically-sensitive field effect transistor (FET) having amulti-layered structure is provided. For instance, thechemically-sensitive FET may include a first layer such as a substratelayer. The substrate layer, like all layers disclosed herein, may havean extended body including a proximal portion having a proximal end, adistal portion having a distal end, and a pair of opposed side portions,all of which together define a circumference for the substrate layer.Additionally, a second layer, e.g., a first non-conductive materiallayer, may be included wherein the first non-conductive material layermay be an insulating layer and be positioned above the extended body ofthe substrate layer. In various embodiments, a second non-conductivematerial layer, which may also be an insulating layer, may also beincluded and positioned above the first non-conductive material layer.

In various embodiments, one or more conductive elements (e.g., composedof an electrically conductive material), such as one or more electrodes,such as a source electrode and a drain electrode for a transistor, maybe provided. In various instances, the conductive elements may beseparated one from the other and positioned within one or more of thenon-conductive layers so as to from a channel between the electrodes. Inparticular embodiments, the source and drain electrodes may have aplanar arrangement and may be in an opposed configuration to oneanother, where one or both of the source and drain electrodes have ageometrical formation or pattern designed to maximize the ratio of thechannel width to channel length. For instance, the source and drainelectrodes may be configured, e.g., within the insulating layer suchthat the channel length is less than about 1000 nm, less than about 500nm, less than about 100 nm, may be less than about 50 nm, or may be lessthan about 10 nm, less than about 5 or 3 nm or less.

Further, in various embodiments, the chemically-sensitive field effecttransistor (FET) may include a well structure, provided at least withinthe first and/or second non-conductive material layers. In such aninstance, the well structure may include a chamber, such as a chamberthat may be bounded by one or more bounding members. For instance, thebounding member may be configured as a plurality of walls or a circularcircumferential surface member. In particular embodiments, the boundingmember(s) and/or the surrounding insulating layer(s) may be configuredto include the source and drain electrodes. For example, one or more,e.g., both of the source and drain electrodes may be configured so as tobe included within a bottom and/or a side surface on the well boundingmember. In such an instance, the source and drain electrodes may beconfigured so as to increase the channel width to length ratio.Particularly, the source and drain electrodes may have athree-dimensional (3D) configuration and may be incorporated on orwithin the bottom surface member of the chamber and/or be incorporatedwithin one or more side or circumferential surface members of thechamber. In such instances, the source and drain electrodes may beconfigured so as to increase the channel width to length ratio by afactor of about 10 or 20 or more, e.g., compared to an electrode patternonly at the bottom of the well, such as by a factor of 100 or more, suchas a geometric electrode pattern that increases the channel width tolength ratio by a factor of 1000 or more.

Particularly, in certain embodiments, the source and drain electrodesmay be separated one from the other by one or more spaces, and thus, maybe configured to not only have a 3D structure but to also be in anopposed but interdigitated relationship to one another. For instance,one or more of the source and drain electrodes may be formed so as toinclude an impingement member, and one or more of the source and drainelectrodes may be formed so as to include a receiving member, such aswhere the impingement member is configured for being inserted within thereceiving member, and the receiving member is configured for receivingthe impingement member, while maintaining a distance between oneanother, such as to form one or more channels there between.

Hence, in various instances, the source and drain electrodes may haveone or more, e.g., a plurality of, prongs or tines so as to give theelectrode a fork like configuration, such as can be seen with respect toFIG. 11, where the tines are capable of being fit one within the otherwhile maintaining a space there between. In such instances, theinterdigitated tines of the source and drain electrodes may be disposedwithin one or both of the first and second non-conductive materiallayers and be separated from one another by a distance so as to form thechannel. In particular embodiments, the bounding member(s) of thechamber may be configured so as to include one or more vias, trenches,or slots that may be formed in the transistor channel material, whichmay then be filled with the electrode material so as to allow the formedelectrodes to not only contact the well surface, but to also be incontact with the channel and/or a material layer designed to form orotherwise augment the channel conductivity. Accordingly, in variousembodiments, a channel material layer may be provided, and the sourceand/or drain electrodes may be configured so as to contact the channelmaterial and/or to also contact an edge of the channel material.

Thus, in various embodiments, the chemically sensitive FET may beconfigured to include a channel, such as a channel that includes or isotherwise composed of a transistor channel material, such as is formedover and/or between the electrodes, e.g., the source and drainelectrodes. For instance, a 1D, 2D, e.g., a graphene layer, and/or 3Dstructured layer, may be positioned between the first and secondnon-conductive material layers. For example, the transistor materialchannel material may be a 1D material may be comprised of carbonnanotubes or semiconducting material such as in a nanowire form, such asincluding Si, Ge or a metal oxide. In other instances, the 2D materialmay be composed of one or more of graphene, Molybdenum disulfide (MoS2),MoSe2, Phosphorene (black phosphorous), Silicene, Borophene, Tungstendisulfide (WS2), Boron Nitride, WSe2, Stanene (2D tin), Graphane,Germanane, Nickel HITP, Mxenes (Ti2C, (Ti0.5,Nb0.5), V2C, Nb2C, Ti3C2,Ti3CN, Nb4C3, Ta4C3), and/or transition metal dichalcogenides. Thetransistor material may be a bulk transistor material such as Si,amorphous Si, Ge, and/or metal oxide. In particular instances, thechannel transistor material may be configured so as to extend between asurface portion of the source electrode and a surface portion of thedrain electrode. In such an instance, positioning of the transistorchannel material between the source and drain electrodes is designed toform the channel and thereby control and/or regulate conductivitybetween the electrodes. Hence, the FET may include a gate structure.

In certain instances, as herein disclosed, the FET may be configured forperforming a chemical reaction, such as for the detection of one or moreanalytes, such as a reactant from a chemical reaction. Accordingly, invarious instances, the FET may include an analyte-sensitive layer. Invarious embodiments, e.g., to facilitate the performance of a chemicalreaction, the field effect transistor may include a well structure,within which a chemical reaction may take place. For instance, one ormore of the layers of the FET, such as the first and/or secondinsulating layers may include a chamber, such as a chamber to which thereactants may be added for the performance of the chemical reaction. Insuch an instance, the gate structure of the FET may be formed within thechamber and over the channel so as to electrically connect the sourceand the drain electrodes. Further, one or more solutions, such ascontaining one or more reactants may be added to the chamber therebyforming a solution gate. In various instances, the gate structure mayinclude the graphene layer.

Further, in various embodiments, the chemically-sensitive field effecttransistor and/or the chamber thereof may be configured such that theelectrodes, e.g., the source and drain electrodes, are positioned on orin the bounding member of the chamber. For instance, in variousinstances, the surfaces or walls of the chamber may include one or moretrenches, wherein the trench includes one or more of the electrodestructures, and/or may include the 1D or 2D structure, such as thegraphene layer. Hence, the electrodes of the source and drain may beincluded in a bottom or side or circumferential surface of the well ortrench. In such an instance, an analyte-sensitive layer may be formed onthe well or trench bottom and/or sidewalls and/or may cover theelectrodes and/or channel material. In some instances, the 1D channelmaterial may be a vertically-oriented 1D channel material. Consequently,the chamber may be configured for sensing and/or measuring the analytesuch as a reactant that results from the reaction taking place withinthe chamber.

For example, one or more surfaces of the substrate and/or a well and/ora chamber thereof may be fabricated in such a manner so as incorporatethe electrodes therein. Particularly, one or more of the electrodesdisclosed herein may be formed by any suitable method, such as by beinglithographically photopatterned, which may utilize a light source and/oroptics that allow patterning of deep trenches and/or wells. Moreparticularly, in various instances, an electron beam, laser or plasmabeam may be utilized to pattern the wells and/or trenches and/or theelectrodes. In various instances, the well structure is comprised ofalternating vertical layers of source and drain electrodes, such as todefine the channel width and the channel length. In particularembodiments, the well structure is comprised of electrodes on a wellbottom and/or in conjunction with alternating vertical layers of sourceand drain electrodes so as to define a channel width and/or channellength. As stated above, the electrodes may have a transistor channelmaterial and/or an analyte-sensitive material over and/or between them,such as in the alternating vertical layer configuration. In variousembodiments, the analyte-sensitive material may be formed by PVDdeposition of a metal and oxidization of that metal and/or theanalyte-sensitive material may be formed by ALD deposition of a metaloxide, such where the PVD deposition is a sputter or e-beam deposition,and/or the oxidation is a thermal or plasma oxidation. In particularinstances, the analyte-sensitive material may be comprised of multiplelayers, which material may be formed by any process or a combination ofprocesses so as to cover a bottom and/or side of the well, and incertain instances, the analyte-sensitive material at the bottom of thewell may be different from the analyte-sensitive layer coating the wellor trench walls.

Accordingly, in a further aspect of the disclosure, a method forproducing a field effect transistor is provided, such as a FET that isconfigured for performing a chemical reaction and sensing one or more ofthe products thereof. In such instances, the FET may include a pluralityof electrodes, and in various instances may be in an alternating,vertical and/or interdigitated layered configuration. In such aninstance, the method may include forming alternating layers of sourceelectrodes, dielectric material and drain electrodes, as well as forminga well or trench within a central portion of the source and drainelectrode patterns. The method may include forming a well or trench inone or more of the layers of the FET, such as one or more of theinsulating layers, such as in an etching process, such as by wet etchingor plasma etching, or the like.

Hence, in various instances, the method for producing a sensor mayinclude forming alternating and/or interdigitated layers of sourceelectrodes, dielectric material, and/or drain electrodes, forming a wellor trench within a central portion of the source and drain electrodepatterns, and/or forming a transistor channel material over or betweenthe source and drain electrodes, such as where an analyte-sensitivelayer may be formed over the transistor channel layer. For instance, afirst layer of transistor channel material may be formed over a firstelectrode layer, a dielectric layer may be formed over the firstelectrode layer, a trench may be patterned in the dielectric layer, asecond electrode layer may then be formed within the trench. In variousembodiments, the second electrode layer and dielectric layer may beplanarized, a second layer of transistor channel material may then beformed over the second electrode and second dielectric layer and thisprocess may then be repeated so as to produce the desired number ofelectrode and channel layers.

A useful detailed description is set forth in van Rooyen et al., U.S.Patent Publication Number 20140371110 for Bioinformatics Systems,Apparatuses, and Methods Executed On An Integrated Circuit ProcessingPlatform, which is “hereby incorporated by reference in its entirety.

Another useful detailed description is set forth in van Rooyen et al.,U.S. Patent Publication Number 20140309944 for Bioinformatics Systems,Apparatuses, and Methods Executed On An Integrated Circuit ProcessingPlatform, which is hereby incorporated by reference in its entirety.

Another useful detailed description is set forth in van Rooyen et al.,U.S. Patent Publication Number 20140236490 for Bioinformatics Systems,Apparatuses, and Methods Executed On An Integrated Circuit ProcessingPlatform, which is hereby incorporated by reference in its entirety.

Another useful detailed description is set forth in van Rooyen et al.,U.S. Patent Publication Number 20140200166 for Bioinformatics Systems,Apparatuses, and Methods Executed On An Integrated Circuit ProcessingPlatform, which is hereby incorporated by reference in its entirety.

Another useful detailed description is set forth in McMillen et al.,U.S. Provisional Patent Application No. 62/127,232, filed on Mar. 2,2015, for Bioinformatics Systems, Apparatuses, And Methods Executed OnAn Integrated Circuit Processing Platform, which is hereby incorporatedby reference in its entirety.

Another useful detailed description is set forth in van Rooyen et al.,U.S. Provisional Patent Application No. 62/119,059, filed on Feb. 20,2015, for Bioinformatics Systems, Apparatuses, And Methods Executed OnAn Integrated Circuit Processing Platform, which is hereby incorporatedby reference in its entirety.

Another useful detailed description is set forth in van Rooyen et al.,U.S. Provisional Patent Application No. 61/988,128, filed on May 2,2014, for Bioinformatics Systems, Apparatuses, And Methods Executed OnAn Integrated Circuit Processing Platform, which is hereby incorporatedby reference in its entirety.

Another useful detailed description of a GFET is set forth in vanRooyen, U.S. Provisional Patent Application No. 62/094,016, filed onDec. 18, 2014, for Graphene FET Devices, Systems, And Methods Of UsingThe Same For Sequencing Nucleic Acids, which is hereby incorporated byreference in its entirety.

Another useful detailed description of a GFET is set forth in Hoffman etal., U.S. Provisional Patent Application No. 62/130,594, filed on Mar.9, 2015, for Chemically Sensitive Field Effect Transistor, which ishereby incorporated by reference in its entirety.

Another useful detailed description of a GFET is set forth in Hoffman etal., U.S. Provisional Patent Application No. 62/130,598, filed on Mar.9, 2015, for Method And System For Analysis Of Biological And ChemicalMaterials, which is hereby incorporated by reference in its entirety.

Another useful method for growing and transferring graphene is disclosedin Hoffman et al., U.S. Provisional Patent Application No. 62/175,351,filed on Jun. 14, 2015, for a System And Method For Growing AndTransferring Graphene For Use As A FET, which is hereby incorporated byreference in its entirety.

Another use for two dimensional materials is disclosed in Hoffman etal., U.S. Provisional Patent Application No. 62/175,384, filed on Jun.14, 2015, for a CMOS Integration OfA Two-Dimensional Material, which ishereby incorporated by reference in its entirety.

The following U.S. Patent Applications discuss the processing componentof the a system for analysis of biological and chemical materials: U.S.patent application Ser. No. 14/279,063, titled, Bioinformatics Systems,Apparatuses, and Methods Executed on an Integrated Circuit ProcessingPlatform, filed May 15, 2014; U.S. patent application Ser. No.14/180,248, titled Bioinformatics Systems, Apparatuses, and MethodsExecuted on an Integrated Circuit Processing Platform, filed Feb. 13,2014; U.S. patent application Ser. No. 14/179,513, titled BioinformaticsSystems, Apparatuses, and Methods Executed on an Integrated CircuitProcessing Platform, filed Feb. 12, 2014; U.S. patent application Ser.No. 14/158,758, titled Bioinformatics Systems, Apparatuses, and MethodsExecuted on an Integrated Circuit Processing Platform, filed Jan. 17,2014; U.S. patent application Ser. No. 14/279,063; U.S. ProvisionalApplication No. 61/826,381, titled System and Method for ComputationGeneomic Pipeline, filed May 22, 2013; U.S. Provisional Application No.61/943,870, titled Dynamic Genome Reference Generation For Improved NGSAccuracy And Reproducibility, filed Feb. 24, 2014; all of which arehereby incorporated by reference in their entireties herein.

From the foregoing it is believed that those skilled in the pertinentart will recognize the meritorious advancement of this invention andwill readily understand that while the present invention has beendescribed in association with a preferred embodiment thereof, and otherembodiments illustrated in the accompanying drawings, numerous changesmodification and substitutions of equivalents may be made thereinwithout departing from the spirit and scope of this invention which isintended to be unlimited by the foregoing except as may appear in thefollowing appended claim. Therefore, the embodiments of the invention inwhich an exclusive property or privilege is claimed are defined in thefollowing appended claims.

The invention claimed is:
 1. A chemically-sensitive field effecttransistor having a multi-layered structure, comprising: a substratelayer, the substrate layer having an extended body; a firstnon-conductive material layer positioned above the extended body of thesubstrate layer; a second non-conductive material layer positioned abovethe first non-conductive material layer; one or more electrode pairscomprising a source electrode and a drain electrode each having a planararrangement and being in an opposed configuration to one another, one orboth of the source and drain electrodes further having an impingementmember, and one or both of the source and drain electrodes having areceiving member, where the impingement member is configured for beinginserted within the receiving member, and the receiving member isconfigured for receiving the impingement member, the source and drainelectrodes being separated from one another by a distance and beingdisposed within one or both of the first and second non-conductivematerial layers, the impingement member and the receiving member of thesource and drain electrodes formed of concentrically curved arcs suchthat at least one pair of the source and drain electrodes has acurvilinear geometric configuration; a graphene layer positioned withinthe distance between the first and second non-conductive material layerand extending between a surface portion of the source electrode and asurface portion of the drain electrode thereby forming a channel betweenthe source and drain electrodes; and a well structure provided at leastwithin the second non-conductive material layer, the well structurehaving a chamber bounded by one or more bounding members, the boundingmembers configured to include the source and drain electrodes as well asthe graphene layer.
 2. The chemically-sensitive field effect transistoraccording to claim 1, wherein at least one of the first and secondnon-conductive material layer comprises an insulating layer.
 3. Thechemically-sensitive field effect transistor according to claim 2,wherein the well structure comprises a gate, the gate formed within thechamber and over the channel so as to electrically connect the sourceand the drain.
 4. The chemically-sensitive field effect transistoraccording to claim 3, wherein the gate comprises a solution gate.
 5. Thechemically-sensitive field effect transistor according to claim 4,wherein the gate comprises the graphene layer.
 6. Thechemically-sensitive field effect transistor according to claim 5,wherein the electrodes are positioned on or in the bounding member ofthe chamber.
 7. A chemically-sensitive field effect transistor having amulti-layered structure, comprising: a substrate layer, the substratelayer having an extended body with a top surface and a bottom surface; afirst non-conductive material layer positioned above the extended bodyof the substrate layer, the first insulating layer having a top surfaceand a bottom surface, the bottom surface of the first insulating layercontacting the top surface of the extended body of the substrate; asecond non-conductive material layer positioned above the firstnon-conductive material layer, the second non-conductive material layerhaving a top surface and a bottom surface, the bottom surface of thesecond non-conductive material layer contacting the top surface of thefirst non-conductive material layer; a well structure provided in atleast the second insulating layer, the well structure having a chamber,the chamber extending inwards from the top surface of the secondinsulating layer toward the top surface of the first insulating layer,the chamber defined by a bounding member; one or more electrode pairscomprising a source and a drain having an interdigitated configurationand being positioned proximate the second insulating layer adjoining thebounding member of the well structure, the source separated from thedrain by a space, the source and drain having a planar arrangementopposed to one another and formed on concentrically curved arcs suchthat at least one pair of the source and drain electrode pairs has acurvilinear geometric configuration; and a graphene layer positioned inthe space between the source and drain electrodes to form a channelthere between.
 8. The chemically-sensitive field effect transistoraccording to claim 7, wherein at least one of the first and secondnon-conductive material layer comprises an insulating layer.
 9. Thechemically-sensitive field effect transistor according to claim 8,wherein the source and drain are formed from electrically conductivematerial.
 10. The chemically-sensitive field effect transistor accordingto claim 9, wherein the well structure comprises a gate, the gate formedwithin the chamber and over the channel so as to electrically connectthe source and the drain.
 11. The chemically-sensitive field effecttransistor according to claim 10, wherein the gate comprises a solutiongate.
 12. The chemically-sensitive field effect transistor according toclaim 11, wherein the gate comprises the graphene layer.
 13. Thechemically-sensitive field effect transistor according to claim 12,wherein the source and drain comprise electrodes, and the electrodes arepositioned on or in the bounding member of the chamber.
 14. Thechemically-sensitive field effect transistor according to claim 12,wherein the source and drain electrodes are positioned on or in thebounding member of the chamber.
 15. A chemically-sensitive field effecttransistor having a multi-layered structure, comprising: a substratelayer, the substrate layer having an extended body; a first insulatinglayer positioned above the extended body of the substrate layer; asecond insulating layer positioned above the first insulating layer andproximate the source and drain electrodes; a well structure provided atleast in the second insulating layer, the well structure having anopening therein, the opening defined by a bounding member; one or moreelectrode pairs comprising a source electrode and a drain electrodepositioned within the second insulating layer proximate the boundingmember, the source electrode separated from the drain electrode by adistance, the source electrode and the drain electrode having a planararrangement opposed to one another and formed on concentrically curvedarcs such that at least one pair of the source and drain electrode pairshas a curvilinear geometric configuration; and a graphene layerpositioned between the source and drain electrodes, to form a channelthereunder.
 16. The chemically-sensitive field effect transistoraccording to claim 15, wherein the gate comprises a solution gate. 17.The chemically-sensitive field effect transistor according to claim 16,wherein the gate comprises the graphene layer.
 18. Achemically-sensitive field effect transistor having a multi-layeredstructure, comprising: a substrate layer, the substrate layer having anextended body; a first insulating layer positioned above the extendedbody of the substrate layer; a second insulating layer positioned abovethe first insulating layer; an opening provided in the second insulatinglayer, the opening defined by a side surface and a bottom surface; oneor more electrode pairs comprising a source electrode and a drainelectrode, the source electrode separated from the drain electrode by adistance, the source electrode and the drain electrode having a planararrangement opposed to one another and formed on concentrically curvedarcs such that at least one pair of the source and drain electrode pairshas a curvilinear geometric configuration; and a graphene layerpositioned within the distance between the source and drain electrodes,the source electrode, the graphene layer, and the drain electrode beingpositioned within one or both of the side surface and the bottom surfacedefining the opening.
 19. The chemically-sensitive field effecttransistor according to claim 18, wherein the gate comprises a solutiongate.
 20. The chemically-sensitive field effect transistor according toclaim 18, wherein the source and drain electrodes are positioned on orin the bounding member of the chamber.
 21. An integrated circuit forperforming a sequencing reaction, the sequencing reaction involving thesequencing of strands of nucleic acids, the integrated circuitcomprising: a substrate; an array of graphene field effect transistorsarranged on the substrate, each of the graphene field effect transistorscomprising: a primary layer forming a base layer; a secondary layer overthe primary layer, the secondary layer being formed of a firstnonconductive material and comprising one or more electrode pairscomprising a source and a drain formed in the first nonconductivematerial, the source and drain being separated from each other by achannel, the source and the drain being formed of an electricallyconductive material, the source and drain having a planar arrangementopposed to one another and formed on concentrically curved arcs suchthat at least one pair of the source and drain electrode pairs has acurvilinear geometric configuration; and a tertiary layer over thesecondary layer, the tertiary layer comprising a gate formed over thechannel to electrically connect the source and the drain, the gate beingformed of a graphene layer, the tertiary layer further comprising asurface structure that overlaps the source and the drain in thesecondary layer, the surface structure further defining a well havingside walls and a bottom that extends over at least a portion of thegraphene layer of the gate so as to form a reaction chamber for theperformance of the sequencing reaction; wherein one or more of thegraphene field effect transistors of the integrated circuit isconfigured for detecting a change in ion concentration by a change incurrent flow from the source to the drain via an activation of thegraphene layer resulting from the performance of the sequencingreaction.
 22. The integrated circuit in accordance with claim 21,further comprising an ion sensitive layer disposed over the portion ofthe graphene layer at the bottom of the well, the ion sensitive layerbeing formed of an ion sensitive material.
 23. The integrated circuit inaccordance with claim 21, wherein the electrically conductive materialthat forms the source and/or the drain is selected from the group ofelectrically conductive materials that consist of: copper, damascene,aluminum, platinum, and gold.
 24. The integrated circuit in accordancewith claim 21, further comprising an ion selective permeable membranepositioned over the graphene layer.
 25. The integrated circuit inaccordance with claim 21, wherein the gate is configured as a solutiongate.
 26. An integrated circuit for performing a sequencing reaction,the sequencing reaction involving the sequencing of strands of nucleicacids, the integrated circuit comprising: a substrate; an array ofgraphene field effect transistors arranged on the substrate, each of thegraphene field effect transistors comprising: a primary layer forming abase layer; an intermediary layer over the primary layer, theintermediary layer being formed of a first nonconductive material andcomprising one or more electrode pairs comprising a source and a drainformed in the first nonconductive material, the source and drain beingseparated from each other by a channel, the source and the drain beingformed of an electrically conductive material, the source and drainhaving a planar arrangement opposed to one another and formed onconcentrically curved arcs such that at least one pair of the source anddrain electrode pairs has a curvilinear geometric configuration; and atertiary layer over the secondary layer, the tertiary layer comprising agate formed over the channel to electrically connect the source and thedrain, the gate being formed of a graphene layer, the tertiary layerfurther comprising a surface structure that overlaps the source and thedrain in the secondary layer, the surface structure further defining awell having side walls and a bottom that extends over at least a portionof the graphene layer of the gate so as to form a reaction chamber forthe performance of the sequencing reaction.
 27. The integrated circuitin accordance with claim 26, further comprising an ion sensitive layerdisposed over the portion of the graphene layer at the bottom of thewell, the ion sensitive layer being formed of an ion sensitive material.28. The integrated circuit in accordance with claim 26, wherein theelectrically conductive material that forms the source and/or the drainis selected from the group of electrically conductive materials thatconsist of: copper, damascene, aluminum, platinum, and gold.
 29. Theintegrated circuit in accordance with claim 26, further comprising anion selective permeable membrane positioned over the graphene layer. 30.The integrated circuit in accordance with claim 26, wherein the gate isconfigured as a solution gate.